So I plugged in my Kobo Aura HD to upload my latest batch of fanfic updates. Nothing went wrong. So I ejected and...
Now it's doing the import process. It shouldn't be doing that as none of the books are new ones, just existing ones being overwritten.
And... now is half of my "to be read" collection is missing, as is all the books that were listed on the front screen.
I plug my Kobo back in. And got a malformed disk image error. I unplug and then after a very long pause the Kobo setup screen appears.
EDIT: All my sideloaded books seem to be intact. So I'm going to to try restore database.