I had somewhat similar problems with mine, that I had books that showed as being on the kobo drive, but the kobo itself didn't show them. I dragged them off the kobo drive and reinstalled them, which worked after a few tries (but not at first). Have you tried more than one method of deleting them? I remember trying several methods- drag-and-drop to trash, right-click and delete, etc., and one of them eventually worked. I also had to reboot the kobo, if I remember correctly.
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