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I think the only thing you can do with your B&N-purchased ebooks is to "archive" them, which will remove them from the Nook itself but preserve them on the B&N server. They may still appear in the list of books in the B&N Nook library however.
Of course, if you are using Calibre on all your B&N books (doing it right after buying them), it seems that you would never have to go into the Nook's B&N area, right? So just ignore it, I'd say.
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