Qubes Drive Not Bootable after removal / reinsertion

I don’t think the boot sector has been deleted (since it’s on the drive that you removed) – I believe the EFI entry has been deleted from the BIOS – I’ve seen this happen on my laptop. I think the computer boots and notice the missing drive/EFI Entry and then removes the entry from the menu.

To add it back to the BIOS/UEFI, you should be able to do:

efibootmgr -c -d /dev/nvme0n1 -p 1 -L "QUBES" -l '\EFI\qubes\grubx64.efi'

from the USB stick.