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Before giving up on Calibre try this:
When you right click on a book in Calibre the context menu has an item called "Remove books->Remove matching books from device". Have you tried using it? I guess it can be used in the same way to overwrite books: First remove the book you want to overwrite from Nook with it, then eject, reconnect and send the book to the Nook anew with Calibre.
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