Home dotfiles reset to earlier period?

Hello All,

So weirded out right now. I was working in Android Studio, and all of a sudden everything went wrong. I am going to outline the events here in case someone can help me restore my system. I wish I could turn back the clock, although nothing critical was lost:

  • I exit Android Studio, and see my desktop files gone
  • I open Vivaldi, and see first welcome page
  • I reboot, and see KDE first welcome page (12:17pm)
  • I reboot to an earlier snapper snapshot, using refind-btrfs. I forgot I only configured snapshots for my @root directory (dumb of me in retrospect). My @home is empty in all snapshots.
  • I reboot to a liveUSB (now).

I looked through my files in my home directory, and found:

  • All files in folders controlled by me (ex. ~/* excluding dotfolders and Desktop, Downloads, etc.) were left untouched
  • Some dotfiles and folders present on my initial install in ~/.config and ~/.local/share were modified at 12:17pm. Based on my fish_history, the last commands made were ones I did a while ago (6+ months) when I configured snapper.
  • Some dotfolders and files were left untouched, like those not on my system when I configured snapper. All KDE dotfiles in .config were “reset.” However, those in .local/kde were left alone.
  • As of now it appears my @/ folder was left 100% alone, except for files that interact with dotfiles in the home user folder.

I have never actually restored from a snapper backup before, and can’t say I am too experienced in that respect. Is there any way to debug this issue, and see if these dotfiles can be retrieved? No critical info was lost, but I want to prevent such issues from happening again.

tail of snapper.log
2023-01-23 10:00:39 MIL libsnapper(64440) Snapper.cc(~Snapper):142 - Snapper destructor
2023-01-23 10:01:09 MIL libsnapper(64440) snapperd.cc(main):315 - Exiting
2023-01-23 11:00:00 MIL libsnapper(2216) snapperd.cc(main):283 - Requesting DBus name
2023-01-23 11:00:00 MIL libsnapper(2216) snapperd.cc(main):298 - Loading snapper configs
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(getConfigs):299 - Snapper get-configs
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(getConfigs):300 - libsnapper version 0.10.4
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(reload):922 - loading file /etc/conf.d/snapper
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:SNAPPER_CONFIGS value:root
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:ALLOW_USERS value:
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:ALLOW_GROUPS value:
2023-01-23 11:00:00 MIL libsnapper(2216) snapperd.cc(main):311 - Listening for method calls and signals
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(Snapper):95 - Snapper constructor
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(Snapper):96 - libsnapper version 0.10.4
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(Snapper):97 - config_name:root disable_filters:false
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:FSTYPE value:btrfs
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:QGROUP value:
2023-01-23 11:00:00 MIL libsnapper(2216) AsciiFile.cc(get_value):1078 - key:SYNC_ACL value:no
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(Snapper):130 - subvolume:/ filesystem:btrfs
2023-01-23 11:00:00 MIL libsnapper(2216) Snapper.cc(loadIgnorePatterns):204 - number of ignore patterns:8
2023-01-23 11:00:00 MIL libsnapper(2216) Snapshot.cc(read):288 - found 32 snapshots
2023-01-23 11:00:00 WAR libsnapper(2216) FileUtils.cc(SDir):91 - THROW: open failed path://.snapshots/949 errno:2 (No such file or directory)
2023-01-23 11:00:00 WAR libsnapper(2216) Btrfs.cc(checkSnapshot):482 - CAUGHT: open failed path://.snapshots/949 errno:2 (No such file or directory)
2023-01-23 11:00:00 WAR libsnapper(2216) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:00:00 WAR libsnapper(2216) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:00:30 MIL libsnapper(2216) Snapper.cc(~Snapper):142 - Snapper destructor
2023-01-23 11:01:00 MIL libsnapper(2216) snapperd.cc(main):315 - Exiting
2023-01-23 11:09:23 MIL libsnapper(5046) snapperd.cc(main):283 - Requesting DBus name
2023-01-23 11:09:23 MIL libsnapper(5046) snapperd.cc(main):298 - Loading snapper configs
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(getConfigs):299 - Snapper get-configs
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(getConfigs):300 - libsnapper version 0.10.4
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(reload):922 - loading file /etc/conf.d/snapper
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:SNAPPER_CONFIGS value:root
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:ALLOW_USERS value:
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:ALLOW_GROUPS value:
2023-01-23 11:09:23 MIL libsnapper(5046) snapperd.cc(main):311 - Listening for method calls and signals
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(Snapper):95 - Snapper constructor
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(Snapper):96 - libsnapper version 0.10.4
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(Snapper):97 - config_name:root disable_filters:false
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:FSTYPE value:btrfs
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:QGROUP value:
2023-01-23 11:09:23 MIL libsnapper(5046) AsciiFile.cc(get_value):1078 - key:SYNC_ACL value:no
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(Snapper):130 - subvolume:/ filesystem:btrfs
2023-01-23 11:09:23 MIL libsnapper(5046) Snapper.cc(loadIgnorePatterns):204 - number of ignore patterns:8
2023-01-23 11:09:23 MIL libsnapper(5046) Snapshot.cc(read):288 - found 33 snapshots
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:23 WAR libsnapper(5046) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 11:09:53 MIL libsnapper(5046) Snapper.cc(~Snapper):142 - Snapper destructor
2023-01-23 11:10:23 MIL libsnapper(5046) snapperd.cc(main):315 - Exiting
2023-01-23 12:00:00 MIL libsnapper(16606) snapperd.cc(main):283 - Requesting DBus name
2023-01-23 12:00:00 MIL libsnapper(16606) snapperd.cc(main):298 - Loading snapper configs
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(getConfigs):299 - Snapper get-configs
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(getConfigs):300 - libsnapper version 0.10.4
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(reload):922 - loading file /etc/conf.d/snapper
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:SNAPPER_CONFIGS value:root
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:ALLOW_USERS value:
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:ALLOW_GROUPS value:
2023-01-23 12:00:00 MIL libsnapper(16606) snapperd.cc(main):311 - Listening for method calls and signals
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(Snapper):95 - Snapper constructor
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(Snapper):96 - libsnapper version 0.10.4
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(Snapper):97 - config_name:root disable_filters:false
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:FSTYPE value:btrfs
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:QGROUP value:
2023-01-23 12:00:00 MIL libsnapper(16606) AsciiFile.cc(get_value):1078 - key:SYNC_ACL value:no
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(Snapper):130 - subvolume:/ filesystem:btrfs
2023-01-23 12:00:00 MIL libsnapper(16606) Snapper.cc(loadIgnorePatterns):204 - number of ignore patterns:8
2023-01-23 12:00:00 MIL libsnapper(16606) Snapshot.cc(read):288 - found 9 snapshots
2023-01-23 12:00:00 WAR libsnapper(16606) FileUtils.cc(SDir):91 - THROW: open failed path://.snapshots/950 errno:2 (No such file or directory)
2023-01-23 12:00:00 WAR libsnapper(16606) Btrfs.cc(checkSnapshot):482 - CAUGHT: open failed path://.snapshots/950 errno:2 (No such file or directory)
2023-01-23 12:00:00 WAR libsnapper(16606) FileUtils.cc(SDir):66 - THROW: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 12:00:00 WAR libsnapper(16606) Hooks.cc(run_scripts):64 - CAUGHT: open failed path:/usr/lib/snapper/plugins errno:2 (No such file or directory)
2023-01-23 12:00:30 MIL libsnapper(16606) Snapper.cc(~Snapper):142 - Snapper destructor
2023-01-23 12:01:00 MIL libsnapper(16606) snapperd.cc(main):315 - Exiting
2023-01-23 12:33:00 MIL libsnapper(2382) snapperd.cc(main):283 - Requesting DBus name
2023-01-23 12:33:00 MIL libsnapper(2382) snapperd.cc(main):298 - Loading snapper configs
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(getConfigs):299 - Snapper get-configs
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(getConfigs):300 - libsnapper version 0.10.4
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(reload):922 - loading file /etc/conf.d/snapper
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:SNAPPER_CONFIGS value:root
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:ALLOW_USERS value:
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:ALLOW_GROUPS value:
2023-01-23 12:33:00 MIL libsnapper(2382) snapperd.cc(main):311 - Listening for method calls and signals
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(Snapper):95 - Snapper constructor
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(Snapper):96 - libsnapper version 0.10.4
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(Snapper):97 - config_name:root disable_filters:false
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(reload):922 - loading file /etc/snapper/configs/root
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:SUBVOLUME value:/
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:FSTYPE value:btrfs
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:QGROUP value:
2023-01-23 12:33:00 MIL libsnapper(2382) AsciiFile.cc(get_value):1078 - key:SYNC_ACL value:no
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(Snapper):130 - subvolume:/ filesystem:btrfs
2023-01-23 12:33:00 MIL libsnapper(2382) Snapper.cc(loadIgnorePatterns):204 - number of ignore patterns:8
2023-01-23 12:33:00 MIL libsnapper(2382) Snapshot.cc(read):288 - found 10 snapshots
2023-01-23 12:33:00 WAR libsnapper(2382) Snapper.cc(calculateUsedSpace):821 - THROW: quota rescan or sync failed
2023-01-23 12:33:00 WAR libsnapper(2382) Client.cc(dispatch):1921 - CAUGHT: quota rescan or sync failed
2023-01-23 12:33:15 WAR libsnapper(2382) Snapper.cc(calculateUsedSpace):821 - THROW: quota rescan or sync failed
2023-01-23 12:33:15 WAR libsnapper(2382) Client.cc(dispatch):1921 - CAUGHT: quota rescan or sync failed
2023-01-23 12:33:45 MIL libsnapper(2382) Snapper.cc(~Snapper):142 - Snapper destructor
2023-01-23 12:34:15 MIL libsnapper(2382) snapperd.cc(main):315 - Exiting
tail of pacman.log
[2023-01-23T11:00:45-0500] [PACMAN] Running 'pacman --sync -y -u --'
[2023-01-23T11:00:45-0500] [PACMAN] synchronizing package lists
[2023-01-23T11:00:47-0500] [PACMAN] starting full system upgrade
[2023-01-23T11:01:19-0500] [ALPM] transaction started
[2023-01-23T11:01:19-0500] [ALPM] upgraded binutils (2.40-1 -> 2.40-2)
[2023-01-23T11:01:19-0500] [ALPM] upgraded boost-libs (1.80.0-3 -> 1.81.0-2)
[2023-01-23T11:01:20-0500] [ALPM] upgraded clucene (2.3.3.4-13 -> 2.3.3.4-14)
[2023-01-23T11:01:20-0500] [ALPM] upgraded graphviz (7.0.6-1 -> 7.1.0-1)
[2023-01-23T11:01:20-0500] [ALPM-SCRIPTLET] Warning: Could not load "/usr/lib/graphviz/libgvplugin_gdk.so.6" - It was found, so perhaps one of its dependents was not.  Try ldd.
[2023-01-23T11:01:20-0500] [ALPM-SCRIPTLET] Warning: Could not load "/usr/lib/graphviz/libgvplugin_gtk.so.6" - It was found, so perhaps one of its dependents was not.  Try ldd.
[2023-01-23T11:01:20-0500] [ALPM-SCRIPTLET] Warning: Could not load "/usr/lib/graphviz/libgvplugin_gdk.so.6" - It was found, so perhaps one of its dependents was not.  Try ldd.
[2023-01-23T11:01:20-0500] [ALPM-SCRIPTLET] Warning: Could not load "/usr/lib/graphviz/libgvplugin_gtk.so.6" - It was found, so perhaps one of its dependents was not.  Try ldd.
[2023-01-23T11:01:20-0500] [ALPM] upgraded imagemagick (7.1.0.57-2 -> 7.1.0.58-1)
[2023-01-23T11:01:21-0500] [ALPM] upgraded imath (3.1.6-1 -> 3.1.6-2)
[2023-01-23T11:01:21-0500] [ALPM] upgraded qt5-multimedia (5.15.8+kde+r1-1 -> 5.15.8+kde+r2-1)
[2023-01-23T11:01:23-0500] [ALPM] upgraded quazip-qt5 (1.3-1 -> 1.4-1)
[2023-01-23T11:01:23-0500] [ALPM] upgraded openimageio (2.4.6.1-3 -> 2.4.6.1-4)
[2023-01-23T11:01:23-0500] [ALPM] upgraded openshadinglanguage (1.12.8.0-2 -> 1.12.8.0-3)
[2023-01-23T11:01:25-0500] [ALPM] upgraded krita (5.1.5-1 -> 5.1.5-2)
[2023-01-23T11:01:25-0500] [ALPM] upgraded libixion (0.17.0-3 -> 0.17.0-4)
[2023-01-23T11:01:25-0500] [ALPM] upgraded liborcus (0.17.2-3 -> 0.17.2-4)
[2023-01-23T11:01:35-0500] [ALPM] upgraded libreoffice-fresh (7.4.4-1 -> 7.4.4-2)
[2023-01-23T11:01:35-0500] [ALPM] upgraded maeparser (1.3.0-2 -> 1.3.0-3)
[2023-01-23T11:01:36-0500] [ALPM] upgraded perl-alien-build (2.76-1 -> 2.77-1)
[2023-01-23T11:01:37-0500] [ALPM] upgraded python-numpy (1.23.5-1 -> 1.23.5-2)
[2023-01-23T11:01:37-0500] [ALPM] upgraded python-validate-pyproject (0.10.1-1 -> 0.10.1-2)
[2023-01-23T11:01:37-0500] [ALPM] upgraded snapper (0.10.4-1 -> 0.10.4-2)
[2023-01-23T11:01:37-0500] [ALPM] upgraded source-highlight (3.1.9-9 -> 3.1.9-10)
[2023-01-23T11:01:37-0500] [ALPM] transaction completed
[2023-01-23T11:01:39-0500] [ALPM] running '30-systemd-daemon-reload.hook'...
[2023-01-23T11:01:40-0500] [ALPM] running '30-systemd-update.hook'...
[2023-01-23T11:01:40-0500] [ALPM] running '30-update-mime-database.hook'...
[2023-01-23T11:01:41-0500] [ALPM] running 'dbus-reload.hook'...
[2023-01-23T11:01:41-0500] [ALPM] running 'detect-old-perl-modules.hook'...
[2023-01-23T11:01:41-0500] [ALPM] running 'gtk-update-icon-cache.hook'...
[2023-01-23T11:01:41-0500] [ALPM] running 'rebuild-detector.hook'...
[2023-01-23T11:01:45-0500] [ALPM] running 'texinfo-install.hook'...
[2023-01-23T11:01:45-0500] [ALPM] running 'update-desktop-database.hook'...
[2023-01-23T11:18:01-0500] [PACMAN] Running 'pacman --sync -- libayatana-appindicator'

I am not sure what caused those files to be modified but snapper doesn’t change those files. It just takes snapshots. If you weren’t taking snapshots of your home subvolume, it probably has nothing to do with snapper of snapshots in general.

Likewise pacman doesn’t change files in your home directory.

If you are already running snapper, setup a config to take timeline snapshots of your home directory.

IMO, those snapshots are much more useful to me than the snapshots of my root.

The only reason I thought it was snapper is the fact that the contents of the files were reset to their contents at the point at which I took my first backup. Probably a coincidence. Maybe a program I was running accidentally ran an xdg-* command that reset all of this? It was every xdg dir that was reset in addition to the files in .config/

I can’t speculate as to what happened or how those files were reset. However, if you didn’t take a snapshot of it in the first place, snapper couldn’t restore over it.