Did you press the details button on the message from calibre? I'd be willing to bet that it shows "database disk image is malformed" or words to that effect. KSM is telling you the database on the device is corrupt. As calibre reads that database when getting the list of books, that is the most likely reason for the error.
Unless you have a backup of the database, the fix is to signout of your Kobo account on the device. This will remove the database and reboot the device. Then it will take you through the setup steps and reload the sideloaded books.
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