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Your are not doing anything wrong. B&N Nooks (I'm assuming it's the same with the Color, I have a Touch) do not export and allow your computer to see books you've downloaded using the Nook itself. Basically anything you've downloaded using the Nook from your B&N library cannot be seen. The Nook hides these files and does not make them accessible to your computer. This prevents calibre from seeing them.
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