Sorry, I don't know what is happening here. If this was a newer Kobo device, I would think it was a corrupt database and suggest logging off the device and back on. This usually fixes problems like this. But, the description of the doesn't match. It would probably be a good idea to test the database. My Kobo utilities plugin has an option to do this. If it does show as corrupt, I think you will have to do a factory reset to fix it.
For sideloaded books, the Kobo devices process them into an internal database. When you delete them using the device, it deletes the database record and the file. When you delete from the device using calibre, it does the same. If something happens and the book is removed but the database entries are still there, the database entries disappear either when you try to open the book or do a restart of the device.
One of the problems with the processing of the books is that if there is a problem with one, it can prevent other books being processed. If you are seeing the processing screen when you try adding books and disconnecting, but they are not in the library, then this is probably the problem. If this is the case, the only thing you can do is remove all the sideloaded books that are not shown in the library on the device and add them in small batches. That should help find the book causing the problem.
|