Had you sent two new books to the device without ejecting it? When you send the books, calibre will show them as on the device, but when the plugin tries to do anything with the database on the device, the books won't be found. They get added to the database as part of the import process when you eject the device.
Other than that, I would need to see a debug log to try and work out which books the plugin thought was missing and why.
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