Those are usually signs of a corrupt database on the device. The database contains details of all the books, the reading status and collections.
The simple fix is to sign out of the Kobo account and then follow the prompts to sign in and set up the device again. The sideloaded books will be added to the database again.
If this doesn't work, do a factory reset. And as this is a new device, I would be tempted to do this and then do the full setup.
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