The implication is that the book "unique ID" is being lost somehow. I don't know how this might happen.
When connected using the wireless device, are the "missing" books visible in calibre's device view? They should be there without the "In Library" check mark. If they are there, what happens if you use calibre's "Match book to library" command? You get to that command by right-clicking on a book. Use "Search" to find the right book in the library. Don't forget to use the "Update cached metadata on device" when done.
Another thing you should do is check calibre's database for integrity. When disconnected from the device, click the Library button, choose Library Maintenance then Check Library.
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