That usually means the database on the device is corrupt. When the database is corrupt, the writes to it do not happen properly. Usually, it keeps working OK until the device is restarted. The database is read at that point, but, the contents are out of date. But, sometimes it works like you are seeing.
The only fixes are to restore a backup, or sign out of the Kobo account and back in. The latter will generate a new database and import your sideloaded books. If this is happening a lot, you might want to do a full factory reset to force a reformat of the book and root partitions. That could solve things. But, with the age of the device, it could be the SD card is failing and causing the writes not to happen properly. Replacing the card would probably solve the problems.
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