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Somehow your database has become corrupted. There are various oopsies that can make this happen, for example, an "unsafe" disconnect or putting the device to sleep when something is being written to the Db.
You will want to get a fresh copy of the Db onto your device. I use the mighty fine Kobo Utility plugin and save a copy of my healthy database fairly often, so I can just replace the baddy with a goody.
If you don't have that option, then sign out of your Kobo account on the device, and sign back in. You will get a fresh DB and the Kobo books and the sideloaded books will reload. Hopefully, you have been updating the %read on calibre (also the Utility Plugin) so you can restore your bookmarks.
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