limine-snapper-watcher won't clean up the pacman lock file if DBPath in /etc/pacman.conf is not the default. From /usr/bin/limine-snapper-watcher:

### Remove pacman lock after restore for Arch Linux & Arch based distros
remove_pacman_lock() {
    if [[ -f /var/lib/pacman/db.lck ]]; then
        if ! pgrep -x pacman &>/dev/null; then
            rm /var/lib/pacman/db.lck
        fi
    fi
}

@Zesko Thank you for clarification! I thought the file inside EFI should not be deleted. Everything works perfectly fine as before now.

@ghorshy

Please do not copy /boot/limine.conf to /boot/EFI/limine/limine.conf. This location has the highest priority and should not be managed by automation. But it is intended only for users or developers who want full control and wish to override automated configurations.

If you want to use automated configuration, remove any other conflicting Limine config files. Keep only the default /boot/limine.conf, which is managed by automated processes and is the easiest for most users to find. Do not hide config files in deep directories.