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Almost sure, that your database is corrupt, if you can log out from menu (sometimes after database corruption I was unable to), then log in, a new database will be created, and books will be re-read again.
If you made backups with calibre, you should copy it back to .kobo directory. (kobo utilities plugin can do it).
You can also try to repair it by any sqlite handling database software, but for me it usually didn't succedd at this stage.
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