I’m going to settle for that.
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.
So since
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.