In an effort to better understand my system, I recently grabbed an old Thinkpad and installed Arch using luks encrypted lvm2 containers. The process is quite similar between uefi and bios and you’ll probably have a better idea about the ideas involved in your re-installation of grub and your system in general. Just a thought…
cryptsetup luksOpen /dev/sdaX crypto ( here volume mapper encrypted )
cryptsetup luksOpen /dev/sdaY swap ( case out encrypted )
mount /dev/mapper/crypto /mnt
mount /dev/sda1 /mnt/boot/efi ( if you need Efi )
mount -t proc proc /mnt/proc
mount -t sysfs sys /mnt/sys
mount -o bind /dev /mnt/dev
mount -t devpts pts /mnt/dev/pts/
I have taken a backup with clonezilla (though I’m not sure it will be able to restore encrypted partitions and MBR without extra problems). I have backups of my data. But I don’t currently have the time to mess with re-installation of the OS or to try and solve future errors that might arise with clonezilla.
I’m going to leave this for later.
I did update my machine with latest updates (without re-installing grub) and everything is fine.
I don’t know if I should mark this as the solution to my original question (since it doesn’t solve the question itself), but this ends my inquiry regarding that issue for the time being.