I see. I just spotted that after fixing up the site. Everything broke since I had moved wordpress to its own directory and changed the prefix of the database. Everything's still there... resolved. Whew!
I jumped the gun on that one a bit, and I've changed the auto-upgrade to 'notify', but I wonder if the auto update script could be modified to check for mods such as what I'd done. That way the upgrade won't break sites that have been modified. Or if that's not feasible, checking to see if there are any mods, and if so, not upgrading but rather just send a notice that upgrading couldn't be performed without checking the mods.
Thanks as always, rlparker, for your prompt advice!