With that description, the database on the device is probably corrupted. When that happens, the device appears to be running OK, but any changes are not written to the database correctly. A restart of the device will do a reread of the database. This will read the corrupt database that doesn't have any recent changes including any added books.
I don't know how the database became corrupted. But, running out of power could be a cause. If the device didn't get a chance to complete writing to the database before it lost power, that would explain it. It would probably depend on exactly what was being done at the time whether this happened.
You can check the database for errors using any SQLite viewer. If you use calibre, my Kobo Utilities plugin has a database check function. But, I would expect that calibre would display an error while trying to get the book list from the device.
If I am correct, the fix is to do a logout on the device and log back in. This takes you through a basic setup which includes removes the current database and creating a fresh one. Then a sync is done to Kobo, to fetch details of the purchased books and any sideloaded books on the device are added.
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