Turns out ssh-agent is the cause of the unknown UUID bug! I got a tip
about this from a user, and was quickly able to reproduce the bug that had
eluded me so long. Anyone who has run `ssh-add` and is using ssh-agent
would see the bug.

It was easy enough to fix as it turns out. Just need to set IdentitiesOnly
in .ssh/config where git-annex has set up its own IdentityFile to ensure
that its special purpose ssh key is used rather than whatever key the
ssh-agent has loaded into it. I do wonder why ssh behaves this way -- why
would I set an IdentityFile for a host if I didn't want ssh to use it?

Spent the rest of the day cleaning up after the bug. Since this affects so
many people, I automated the clean up process. The webapp will
detect repositories with this problem, and the user just has to click to
clean up. It'll then correct their .ssh/config and re-enable the
repository.