Well, the last easy idea I had has now failed.

I've ordered a new M.2 drive that will be here by the 25th. I'm going to do a fresh install to the new drive, which should set up all the EFI vars.

Then I'm going to swap my current drive back in and see if it'll boot that way.

If not, I'll switch back to the new drive, restore from the latest proper backup and then manually go through the files that may have changed between the proper backup and the copying files around that I did today.

Now I just have to wait for the M.2 drive to arrive. If this works, it'll validate me not liking the design of UEFI (hiding variables in the BIOS instead of putting everything on the bootable media).