All USB devices missing with LTS kernel

Due to a potential problem with VMware Workstation not working with the 6.9 kernel (see https://github.com/mkubecek/vmware-host-modules/issues/239), I installed the LTS kernel. When I rebooted, my system did not see any of the USB devices: keyboard, mouse, SSDs. And since this system is installed on a USB-attached SSD, it did not boot. I don’t think I’ve ever seen this before.

Here are my relevant configs/system info:
/boot/grub/grub.cfg

#
# DO NOT EDIT THIS FILE
#
# It is automatically generated by grub-mkconfig using templates
# from /etc/grub.d and settings from /etc/default/grub
#

### BEGIN /etc/grub.d/00_header ###
if [ -s $prefix/grubenv ]; then
  load_env
fi
if [ "${next_entry}" ] ; then
   set default="${next_entry}"
   set next_entry=
   save_env next_entry
   set boot_once=true
else
   set default="0"
fi

if [ x"${feature_menuentry_id}" = xy ]; then
  menuentry_id_option="--id"
else
  menuentry_id_option=""
fi

export menuentry_id_option

if [ "${prev_saved_entry}" ]; then
  set saved_entry="${prev_saved_entry}"
  save_env saved_entry
  set prev_saved_entry=
  save_env prev_saved_entry
  set boot_once=true
fi

function savedefault {
  if [ -z "${boot_once}" ]; then
    saved_entry="${chosen}"
    save_env saved_entry
  fi
}

function load_video {
  if [ x$feature_all_video_module = xy ]; then
    insmod all_video
  else
    insmod efi_gop
    insmod efi_uga
    insmod ieee1275_fb
    insmod vbe
    insmod vga
    insmod video_bochs
    insmod video_cirrus
  fi
}

insmod part_gpt
insmod btrfs
search --no-floppy --fs-uuid --set=root bdd04bd5-f872-4915-ab50-3d3429048bbf
if loadfont /@/usr/share/grub/ter-u18n.pf2 ; then
  set gfxmode=1920x1080x32
  load_video
  insmod gfxterm
  set locale_dir=$prefix/locale
  set lang=en_US
  insmod gettext
fi
terminal_input console
terminal_output gfxterm
insmod part_gpt
insmod btrfs
search --no-floppy --fs-uuid --set=root bdd04bd5-f872-4915-ab50-3d3429048bbf
insmod gfxmenu
loadfont ($root)/@/boot/grub/themes/darkmatter/ter-u16n.pf2
loadfont ($root)/@/boot/grub/themes/darkmatter/ter-u18n.pf2
loadfont ($root)/@/boot/grub/themes/darkmatter/ter-u20n.pf2
loadfont ($root)/@/boot/grub/themes/darkmatter/ter-u22n.pf2
insmod png
set theme=($root)/@/boot/grub/themes/darkmatter/theme.txt
export theme
if [ x$feature_timeout_style = xy ] ; then
  set timeout_style=menu
  set timeout=5
# Fallback normal timeout code in case the timeout_style feature is
# unavailable.
else
  set timeout=5
fi
### END /etc/grub.d/00_header ###

### BEGIN /etc/grub.d/10_linux ###
menuentry 'EndeavourOS Linux, with Linux linux' --class endeavouros --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-linux-advanced-bdd04bd5-f872-4915-ab50-3d3429048bbf' {
	load_video
	set gfxpayload=keep
	insmod gzio
	insmod part_gpt
	insmod btrfs
	search --no-floppy --fs-uuid --set=root bdd04bd5-f872-4915-ab50-3d3429048bbf
	echo	'Loading Linux linux ...'
	linux	/@/boot/vmlinuz-linux root=UUID=bdd04bd5-f872-4915-ab50-3d3429048bbf rw rootflags=subvol=@  nowatchdog nvme_load=YES nvidia-drm.modeset=1 loglevel=3 iommu=pt split_lock_detect=off
	echo	'Loading initial ramdisk ...'
	initrd	/@/boot/intel-ucode.img /@/boot/initramfs-linux.img
}

### END /etc/grub.d/10_linux ###

### BEGIN /etc/grub.d/20_linux_xen ###
### END /etc/grub.d/20_linux_xen ###

### BEGIN /etc/grub.d/25_bli ###
if [ "$grub_platform" = "efi" ]; then
  insmod bli
fi
### END /etc/grub.d/25_bli ###

### BEGIN /etc/grub.d/40_custom ###
# This file provides an easy way to add custom menu entries.  Simply type the
# menu entries you want to add after this comment.  Be careful not to change
# the 'exec tail' line above.

# Microsoft Windows installations
menuentry 'Windows 11 Systems [Gaming, Hyper-V Testing]' --class windows11 {
	search --fs-uuid --no-floppy --set=root 4643-8EA0
	echo  'Loading Windows 11 Bootmanager ...'
	chainloader (${root})/EFI/Microsoft/Boot/bootmgfw.efi
}

# maintenance setups
# NOTE: need to add one for memtest86+

menuentry 'UEFI Firmware Settings' $menuentry_id_option 'uefi-firmware' --class settings {
    fwsetup
}

menuentry '' {
    true
}

# other virtual machine hosts
menuentry 'VMHOST-VBOX [vmlinux-linux]' --class virtualbox {
	load_video
	set gfxpayload=keep
	insmod gzio
	insmod part_gpt
	insmod btrfs
	search --no-floppy --fs-uuid --set=root 183c5c34-6d51-418a-b3a1-db1bda7a8f89
	echo	'Loading VMHOST-VBOX ...'
	linux	/boot/vmlinuz-linux root=UUID=183c5c34-6d51-418a-b3a1-db1bda7a8f89 rw nowatchdog nvme_load=YES nvidia-drm.modeset=1 loglevel=3 iommu=pt split_lock_detect=off
	echo	'Loading initial ramdisk ...'
	initrd	/boot/intel-ucode.img /boot/initramfs-linux.img
}

menuentry 'VMHOST-VMWARE [vmlinux-linux]' --class vmware-workstation {
	load_video
	set gfxpayload=keep
	insmod gzio
	insmod part_gpt
	insmod btrfs
	search --no-floppy --fs-uuid --set=root e946d336-6234-4f63-b0e9-535905679ad0
	echo	'Loading VMHOST-VMWARE ...'
	linux	/boot/vmlinuz-linux root=UUID=e946d336-6234-4f63-b0e9-535905679ad0 rw nowatchdog nvme_load=YES nvidia-drm.modeset=1 loglevel=3 iommu=pt split_lock_detect=off
	echo	'Loading initial ramdisk ...'
	initrd	/boot/intel-ucode.img /boot/initramfs-linux.img
}

menuentry 'VMHOST-VMWARE [vmlinux-linux-lts]' --class vmware-workstation {
	load_video
	set gfxpayload=keep
	insmod gzio
	insmod part_gpt
	insmod btrfs
	search --no-floppy --fs-uuid --set=root e946d336-6234-4f63-b0e9-535905679ad0
	echo	'Loading VMHOST-VMWARE ...'
	linux	/boot/vmlinuz-linux-lts root=UUID=e946d336-6234-4f63-b0e9-535905679ad0 rw nowatchdog nvme_load=YES nvidia-drm.modeset=1 loglevel=3 iommu=pt split_lock_detect=off
	echo	'Loading initial ramdisk ...'
	initrd	/boot/intel-ucode.img /boot/initramfs-linux.img
}

menuentry '' {
    true
}

# tested successfully on 2024-04-28
menuentry 'Clonezilla 3.1.2-22 [Live]' --class clonezilla {
    search --fs-uuid --no-floppy --set=root 30d3cf12-d8c7-4722-91a5-97c8797e7fe2
    set isofile='/iso-images/clonezilla-live-3.1.2-22-amd64.iso'
    loopback loop (${root})${isofile}
    linux (loop)/live/vmlinuz boot=live union=overlay username=user config components quiet noswap edd=on nomodeset enforcing=0 locales=en_US.UTF-8 keyboard-layouts=NONE ocs_live_run="ocs-live-general" ocs_live_extra_param="" ocs_live_batch="no" ip= net.ifnames=0 splash vga=795 i915.blacklist=yes radeonhd.blacklist=yes nouveau.blacklist=no vmwgfx.enable_fbdev=1 toram=filesystem.squashfs findiso=${isofile}
    initrd (loop)/live/initrd.img
}

# tested successfully on 2024-04-28
menuentry 'Clonezilla 3.1.2-22 [Autoclone - EndeavourOS/Windows 11]' --class clonezilla {
    search --fs-uuid --no-floppy --set=root 30d3cf12-d8c7-4722-91a5-97c8797e7fe2
    set isofile='/iso-images/clonezilla-live-3.1.2-22-amd64.iso'
    loopback loop (${root})${isofile}
    linux (loop)/live/vmlinuz boot=live union=overlay username=user config components quiet noswap edd=on nomodeset enforcing=0 locales=en_US.UTF-8 keyboard-layouts=NONE ocs_prerun="mount UUID=f8720762-7adf-415b-8641-840da5b958be -o subvol=/,noatime,compress=zstd /mnt" ocs_prerun1="mount --bind /mnt/images/eos-win /home/partimag/" ocs_live_run="ocs-sr -q2 -j2 -z0 -sfsck -senc -p poweroff --batch savedisk autoname-eos-win-year-month-day PTUUID=906A029C-D1F2-43A1-A6ED-3030A0197559" ocs_live_extra_param="" ocs_live_batch="yes" ip= net.ifnames=0 splash vga=795 i915.blacklist=yes radeonhd.blacklist=yes nouveau.blacklist=no vmwgfx.enable_fbdev=1 toram=filesystem.squashfs findiso=${isofile}
    initrd (loop)/live/initrd.img
}

menuentry 'Clonezilla 3.1.2-22 [Autoclone - Virtual Machine Hosts]' --class clonezilla {
    search --fs-uuid --no-floppy --set=root 30d3cf12-d8c7-4722-91a5-97c8797e7fe2
    set isofile='/iso-images/clonezilla-live-3.1.2-22-amd64.iso'
    loopback loop (${root})${isofile}
    linux (loop)/live/vmlinuz boot=live union=overlay username=user config components quiet noswap edd=on nomodeset enforcing=0 locales=en_US.UTF-8 keyboard-layouts=NONE ocs_prerun="mount UUID=f8720762-7adf-415b-8641-840da5b958be -o subvol=/,noatime,compress=zstd /mnt" ocs_prerun1="mount --bind /mnt/images/vm-hosts /home/partimag/" ocs_live_run="ocs-sr -q2 -j2 -z0 -sfsck -senc -p poweroff --batch savedisk autoname-vm-hosts-year-month-day PTUUID=3F2A18F9-F724-4FDF-9ECE-F24807867BCA" ocs_live_extra_param="" ocs_live_batch="yes" ip= net.ifnames=0 splash vga=795 i915.blacklist=yes radeonhd.blacklist=yes nouveau.blacklist=no vmwgfx.enable_fbdev=1 toram=filesystem.squashfs findiso=${isofile}
    initrd (loop)/live/initrd.img
}
### END /etc/grub.d/40_custom ###

### BEGIN /etc/grub.d/41_custom ###
if [ -f  ${config_directory}/custom.cfg ]; then
  source ${config_directory}/custom.cfg
elif [ -z "${config_directory}" -a -f  $prefix/custom.cfg ]; then
  source $prefix/custom.cfg
fi
### END /etc/grub.d/41_custom ###

inxi -Faz

System:
  Kernel: 6.8.9-arch1-2 arch: x86_64 bits: 64 compiler: gcc v: 14.1.1
    clocksource: tsc avail: acpi_pm parameters: BOOT_IMAGE=/@/boot/vmlinuz-linux
    root=UUID=bdd04bd5-f872-4915-ab50-3d3429048bbf rw rootflags=subvol=@
    nowatchdog nvme_load=YES nvidia-drm.modeset=1 loglevel=3 iommu=pt
    split_lock_detect=off
  Desktop: Cinnamon v: 6.0.4 tk: GTK v: 3.24.41 wm: Muffin v: 6.0.1 tools:
    avail: cinnamon-screensaver vt: 7 dm: LightDM v: 1.32.0 Distro: EndeavourOS
    base: Arch Linux
Machine:
  Type: Desktop System: ASUS product: N/A v: N/A serial: <superuser required>
  Mobo: ASUSTeK model: PRIME B760M-A AX v: Rev 1.xx
    serial: <superuser required> part-nu: SKU uuid: <superuser required>
    UEFI: American Megatrends v: 1641 date: 02/21/2024
CPU:
  Info: model: 13th Gen Intel Core i5-13400F bits: 64 type: MST AMCP
    arch: Raptor Lake gen: core 13 level: v3 note: check built: 2022+
    process: Intel 7 (10nm) family: 6 model-id: 0xBF (191) stepping: 2
    microcode: 0x34
  Topology: cpus: 1x cores: 10 mt: 6 tpc: 2 st: 4 threads: 16 smt: enabled
    cache: L1: 864 KiB desc: d-4x32 KiB, 6x48 KiB; i-6x32 KiB, 4x64 KiB
    L2: 9.5 MiB desc: 6x1.2 MiB, 1x2 MiB L3: 20 MiB desc: 1x20 MiB
  Speed (MHz): avg: 800 high: 801 min/max: 800/4600:3300 scaling:
    driver: intel_pstate governor: powersave cores: 1: 800 2: 800 3: 800 4: 800
    5: 800 6: 800 7: 801 8: 800 9: 800 10: 800 11: 800 12: 800 13: 800 14: 800
    15: 800 16: 800 bogomips: 79888
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Vulnerabilities:
  Type: gather_data_sampling status: Not affected
  Type: itlb_multihit status: Not affected
  Type: l1tf status: Not affected
  Type: mds status: Not affected
  Type: meltdown status: Not affected
  Type: mmio_stale_data status: Not affected
  Type: reg_file_data_sampling mitigation: Clear Register File
  Type: retbleed status: Not affected
  Type: spec_rstack_overflow status: Not affected
  Type: spec_store_bypass mitigation: Speculative Store Bypass disabled via
    prctl
  Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer
    sanitization
  Type: spectre_v2 mitigation: Enhanced / Automatic IBRS; IBPB:
    conditional; RSB filling; PBRSB-eIBRS: SW sequence; BHI: BHI_DIS_S
  Type: srbds status: Not affected
  Type: tsx_async_abort status: Not affected
Graphics:
  Device-1: NVIDIA AD107 [GeForce RTX 4060] vendor: ZOTAC driver: nvidia
    v: 550.78 alternate: nouveau,nvidia_drm non-free: 550.xx+
    status: current (as of 2024-04) arch: Lovelace code: AD1xx
    process: TSMC n4 (5nm) built: 2022+ pcie: gen: 1 speed: 2.5 GT/s lanes: 8
    link-max: gen: 4 speed: 16 GT/s ports: active: none off: DP-3,HDMI-A-1
    empty: DP-1,DP-2 bus-ID: 01:00.0 chip-ID: 10de:2882 class-ID: 0300
  Display: x11 server: X.Org v: 21.1.13 with: Xwayland v: 23.2.6 driver: X:
    loaded: nvidia unloaded: modesetting alternate: fbdev,nouveau,nv,vesa
    gpu: nvidia,nvidia-nvswitch display-ID: :0 screens: 1
  Screen-1: 0 s-res: 3840x1080 s-dpi: 81 s-size: 1204x343mm (47.40x13.50")
    s-diag: 1252mm (49.29")
  Monitor-1: DP-3 mapped: DP-4 note: disabled pos: primary,right
    model: Acer XF270H B serial: <filter> built: 2019 res: 1920x1080 hz: 144
    dpi: 82 gamma: 1.2 size: 598x336mm (23.54x13.23") diag: 686mm (27")
    ratio: 16:9 modes: max: 1920x1080 min: 640x480
  Monitor-2: HDMI-A-1 mapped: HDMI-0 note: disabled pos: left
    model: Acer XF270H B serial: <filter> built: 2019 res: 1920x1080 hz: 144
    dpi: 82 gamma: 1.2 size: 598x336mm (23.54x13.23") diag: 686mm (27")
    ratio: 16:9 modes: max: 1920x1080 min: 640x480
  API: EGL v: 1.5 hw: drv: nvidia platforms: device: 0 drv: nvidia device: 2
    drv: swrast gbm: drv: nvidia surfaceless: drv: nvidia x11: drv: nvidia
    inactive: wayland,device-1
  API: OpenGL v: 4.6.0 compat-v: 4.5 vendor: nvidia mesa v: 550.78
    glx-v: 1.4 direct-render: yes renderer: NVIDIA GeForce RTX 4060/PCIe/SSE2
    memory: 7.81 GiB
Audio:
  Device-1: Intel Raptor Lake High Definition Audio vendor: ASUSTeK
    driver: snd_hda_intel v: kernel alternate: snd_sof_pci_intel_tgl
    bus-ID: 00:1f.3 chip-ID: 8086:7a50 class-ID: 0403
  Device-2: NVIDIA vendor: ZOTAC driver: snd_hda_intel v: kernel pcie:
    gen: 4 speed: 16 GT/s lanes: 8 bus-ID: 01:00.1 chip-ID: 10de:22be
    class-ID: 0403
  API: ALSA v: k6.8.9-arch1-2 status: kernel-api
    tools: alsactl,alsamixer,amixer
  Server-1: PipeWire v: 1.0.6 status: active with: 1: pipewire-pulse
    status: active 2: wireplumber status: active 3: pipewire-alsa type: plugin
    4: pw-jack type: plugin tools: pactl,pw-cat,pw-cli,wpctl
Network:
  Device-1: Realtek RTL8125 2.5GbE vendor: ASUSTeK driver: r8169 v: kernel
    pcie: gen: 2 speed: 5 GT/s lanes: 1 port: 5000 bus-ID: 05:00.0
    chip-ID: 10ec:8125 class-ID: 0200
  IF: enp5s0 state: down mac: <filter>
  Device-2: Realtek RTL8852BE PCIe 802.11ax Wireless Network
    vendor: AzureWave driver: rtw89_8852be v: kernel pcie: gen: 1
    speed: 2.5 GT/s lanes: 1 port: 4000 bus-ID: 06:00.0 chip-ID: 10ec:b852
    class-ID: 0280
  IF: wlan0 state: up mac: <filter>
  IF-ID-1: virbr0 state: down mac: <filter>
  Info: services: NetworkManager, nfsd, systemd-timesyncd, wpa_supplicant
Bluetooth:
  Device-1: IMC Networks Bluetooth Radio driver: btusb v: 0.8 type: USB
    rev: 1.0 speed: 12 Mb/s lanes: 1 mode: 1.1 bus-ID: 1-14:10
    chip-ID: 13d3:3571 class-ID: e001 serial: <filter>
  Report: btmgmt ID: hci0 rfk-id: 0 state: down bt-service: enabled,running
    rfk-block: hardware: no software: yes address: <filter> bt-v: 5.3 lmp-v: 12
    status: discoverable: no pairing: no
RAID:
  Hardware-1: Intel Volume Management Device NVMe RAID Controller driver: vmd
    v: 0.6 port: N/A bus-ID: 00:0e.0 chip-ID: 8086:467f rev: class-ID: 0104
Drives:
  Local Storage: total: 6.8 TiB used: 1.05 TiB (15.4%)
  SMART Message: Unable to run smartctl. Root privileges required.
  ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Western Digital
    model: WD Blue SN580 1TB size: 931.51 GiB block-size: physical: 512 B
    logical: 512 B speed: 63.2 Gb/s lanes: 4 tech: SSD serial: <filter>
    fw-rev: 281010WD temp: 33.9 C scheme: GPT
  ID-2: /dev/sda maj-min: 8:0 vendor: SanDisk model: SSD PLUS 480GB
    size: 447.13 GiB block-size: physical: 512 B logical: 512 B type: USB
    rev: 3.2 spd: 5 Gb/s lanes: 1 mode: 3.2 gen-1x1 tech: SSD serial: <filter>
    fw-rev: 1.02 scheme: GPT
  SMART Message: Unknown USB bridge. Flash drive/Unsupported enclosure?
  ID-3: /dev/sdb maj-min: 8:16 vendor: Western Digital
    model: WD40EZRZ-00GXCB0 size: 3.64 TiB block-size: physical: 4096 B
    logical: 512 B type: USB rev: 3.0 spd: 5 Gb/s lanes: 1 mode: 3.2 gen-1x1
    tech: HDD rpm: 5400 serial: <filter> fw-rev: 3002 scheme: GPT
  ID-4: /dev/sdc maj-min: 8:32 vendor: Samsung model: SSD 870 EVO 2TB
    size: 1.82 TiB block-size: physical: 512 B logical: 512 B type: USB rev: 2.1
    spd: 480 Mb/s lanes: 1 mode: 2.0 tech: SSD serial: <filter> fw-rev: 1.02
    scheme: GPT
  SMART Message: Unknown USB bridge. Flash drive/Unsupported enclosure?
Partition:
  ID-1: / raw-size: 329.5 GiB size: 329.5 GiB (100.00%)
    used: 58.47 GiB (17.7%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
  ID-2: /boot/efi raw-size: 2 GiB size: 1.99 GiB (99.61%)
    used: 27.4 MiB (1.3%) fs: vfat dev: /dev/nvme0n1p1 maj-min: 259:1
  ID-3: /home raw-size: 329.5 GiB size: 329.5 GiB (100.00%)
    used: 58.47 GiB (17.7%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
  ID-4: /var/log raw-size: 329.5 GiB size: 329.5 GiB (100.00%)
    used: 58.47 GiB (17.7%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
Swap:
  Kernel: swappiness: 10 (default 60) cache-pressure: 50 (default 100)
    zswap: yes compressor: zstd max-pool: 20%
  ID-1: swap-1 type: file size: 32 GiB used: 0 KiB (0.0%) priority: -2
    file: /.swap/swapfile
Sensors:
  System Temperatures: cpu: 32.0 C mobo: 30.0 C gpu: nvidia temp: 31 C
  Fan Speeds (rpm): fan-1: 926 fan-2: 856 fan-3: 968 fan-4: 944 gpu: nvidia
    fan: 34%
Info:
  Memory: total: 32 GiB note: est. available: 31.13 GiB used: 2.31 GiB (7.4%)
  Processes: 436 Power: uptime: 8m states: freeze,mem,disk suspend: deep
    avail: s2idle wakeups: 0 hibernate: platform avail: shutdown, reboot,
    suspend, test_resume image: 12.41 GiB services: csd-power,
    power-profiles-daemon, upowerd Init: systemd v: 255 default: graphical
    tool: systemctl
  Packages: 1781 pm: nix-default pkgs: 87 pm: nix-sys pkgs: 0 pm: nix-usr
    pkgs: 452 libs: 141 pm: pacman pkgs: 1242 libs: 304 tools: pacseek,yay
    Compilers: gcc: 14.1.1 Shell: fish v: 3.7.1 default: Bash v: 5.2.26
    running-in: xfce4-terminal inxi: 3.3.34

I’ve tested my main EOS system with the LTS kernel and it works fine (installed on NVMe device).

For those interested, the solution was fairly simple. In the boot entry for the LTS kernel, I was trying to load the mainline initrd instead of the LTS one:

linux	/boot/vmlinuz-linux-lts ...
initrd	/boot/intel-ucode.img /boot/initramfs-linux.img

Changing the initrd line to initrd /boot/intel-ucode.img /boot/initramfs-linux-lts.img fixed the USB issue.

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