Well, it worked for a bit, then I discovered today that after deleting a couple of books and adding some new ones with Calibre, my Kobo Touch wouldn't update properly, and I couldn't find the new books on the Kobo. So I did a cold start, and sure enough, database corruption, so I'm doing another factory reset and reloading my library... again.
This is really annoying. Is it Calibre that's causing the error? Or is everybody running into this problem regardless of what program they use to manage their library?
I guess the solution for now is to just not manage the library until Kobo releases a fix.