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I'll assume that you deleted the duplicates from your library. If so, when the device is attached look to the device view in Calibre. You should see an In Library column. Sort on this and those books not in your library should be the ones you want to delete. You may find a few surprises in there so exercise some caution. You do have the option to import these into your library if the surprise is a good one. I did all this just now and found some books I purchased from Kobo that never made it to my Calibre library.
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