I think you have two choices:
- Logout on the device. This will replace the current database with a fresh one and take you through the basic setup. This fixes a lot of these types of problems. After the login, the sideloaded books will be added back to the library.
- A factory reset. This will format the user partition, install the factory firmware and take you through the setup including downloading the latest firmware. You will need to sideload the books afterwards.
Based on the description, I think I would bite the bullet and do the factory reset.
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