Hello, as a newbie here (I have been using EOS for about 1 months and Linux for about 4-5 months), recently I tried to replace Android x86 on my triple boot Linux Mint/Android x86/EOS with Prime OS, but due to some bugs in the Prime OS, my main SSD containing LInux Mint and EOS boot partition (my second hard disk on caddy adapter cannot boot) being wiped, and there’re also some new folders on my second disk as well.
I tried to reinstall Linux Mint and than arch-chroot to my EOS using live USB flash drive to reinstall linux, linux-lts, and grub and change fstab and luckily can got to my EOS system (and it seems that my window manager didn’t break tho), but how to know if there’s a way to check for broken packages without checking for each one), idk where I can post so I posted here.
Welcome to the forum! 
Files on a disk can be broken in many ways.
You can start by checking the pacman database (see man pacman for more info):
pacman -Dkk
I tried that command in the Arch Wiki and it seemed only one package had its files missing, and reinstalled it again. But I wander if you have a Rsync backup file, is there any command to check for any difference between current systems and that file without extract the backup file?
I assume you mean a command that lists all currently installed packages?
# list all installed native packages (and direct the list to a file)
pacman -Qn > native.txt
# lists all installed foreign (=typically from AUR) packages
pacman -Qm > foreign.txt
More info: man pacman
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