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It sounds like your database is corrupt. You can try checking it with Calibre, but unless you have a backup, you may have to delete it (which will erase everything you've saved in every book). If Calibre says it's corrupt, you might be able to repair it with an SQL editor, but restoring a known good backup would be the best option.
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Received this from the database check:
Result of running 'PRAGMA integrity_check' on database on the Kobo device:
ok
Is there something else that could be causing this issue?