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That error means the database on the device is corrupt. The device can usually keep running as for most functions, it is using an in-memory copy the data. But, writes to the database will probably fail. And if you restart the device, it will be reading the data from the last time it was successfully written. That usually means you lose reading status, or new books disappear and have to be reimported.
Unfortunately, there is no way to repair the database. Unless you have a recent backup of the database, the solution is to sign out of the Kobo account on the device, and then do the setup again. This will remove the current corrupt database and build a new one. It will then download the details of any purchased books and reimport any sideloaded books. It does mean you will lose the reading status and annotations for sideloaded books.
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