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Do you have Kobo Utilities? It'll tell you if the KoboReader.sqlite file is malformed when it attempts to backup.
Unfortunately if it is and you don't have an uncorrupted backup you'll have to do a logout-login in the Kobo settings to re-initialize the db. This will re-import any sideloaded books but you'll lose reading positions and annotations that have not been synced to the server (e.g. sideloaded materials).
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