I think I've found another way that one may unwittingly corrupt the database on their kobo. It does occasionally happen that I have both the Kobo desktop and Calibre on. In general, if I eject the device from Calibre, the device appears as ejected from the desktop app,
but not always. So I think I messed up my database once thinking I had ejected correctly via Calibre, without checking all was well in the Kobo desktop.
The short of it is, check that the device appears as ejected from both if you have both running (or "double eject", once from each application - not sure whether ejecting from Calibre and closing down the desktop app also works, but I am not willing to try
)