The calibre error means the database on the device is corrupted. The other problems are symptoms of this. How, it was corrupted is a question. The most likely way is not ejecting the device properly when connected to a PC.
The simplest fix is to logoff on the device. This will wipe the old database and create a new one. It will restart, let you login again and download books from Kobo. Then it will add all the sideloaded books into the library. Unfortunately, you will lose the reading state for sideloaded books.
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