Pulled the SD card after ejecting volumes, plugged it back in, Calibre was fine. Didn't whine about the database or anything. I just don't keep books there really except some news feeds that I didn't clean up yet. (I hate when the database blows up and I have to reinitialize the device so I made that as painless as I could by putting all my books and stuff on the SD card so I don't have to copy it all back.)
Eject successful, Kobo comes back up to Nickle or whatever, and I insert the card with no new books on it since the last time I managed it successfully.
Time to complete: About 60 seconds. Fumbled with the card a bit so give or take 5 seconds.
Plugged it back in for Calibre and… crickets:
ERROR__Error, on Flickr
Same drill. If I attempt a database operation it's def trying to hit the card and not the internal storage.