Sounds like some free classics. They would have been in the ".kobo/kepub" directory. If you rename them to have the extension "epub", they will probably open with the calibre viewer.
I can't think of why they would appear in the calibre device list but not on the device. The calibre device list is read from the database on the Kobo device. I should be able to tell what is happening by looking at the database on the device. But, as you have managed to delete the books, it is probably to late. I would still like to look at it if you are willing to send me the database.