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What did Kobo actually tell you to do? Did they say to sign out of your account on the device? Or did they say to do a factory reset? And, is there any reason you didn't actually do one of these things? I mean, they are the only ways to fix the problem you have. The sign out will probably work, but, it might be necessary to do the full factory reset.
For the record, the database on the device is almost definitely corrupt. The behaviour you describe is what I would expect from a corrupted database. I am a little surprised the Kobo desktop application didn't complain, but, it does depend on exactly what part of the database is corrupt. If you want to check, you can use an SQLite database manager to test the database. Or, if you are a calibre user, my Kobo Utilities plugin can test it.
About the only alternative I can think of is that the internal storage is failing. That would cause a corrupt database and other behaviour as well. But, the first test for this is what I suggest above. If it keeps recurring, then you look at the storage.
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