This seems related to missing systemd-boot-created files.
I believe those errors come from sbctl-batch-sign and the active systemd-boot-update.service trying to access files that don’t exist.
In case the standard EFI path /boot/EFI/BOOT/BOOTX64.EFI doesn’t exist on your UEFI system, you can run sudo limine-install --fallback once.
This installs and keeps a fallback bootloader on the boot partition. It’s useful because most UEFI systems (for example, buggy MSI BIOS firmware) will automatically look for this bootloader if custom boot entries get wiped.