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The books on the Nook are stored on a hidden folder. That is why you do not see them.
If you delete a book, it wil be removed from your B&N account, and you will have to buy it again if you ever want to download a new copy from B&N again.
What I would do is create a new B&N account using another e-mail adress (for example from gmail). Erase and deregister your Nook, and register it again with the new account. This will remove all B&N content from the Nook, and as the new account has an empty library nothing will be syn'ed to your Nook.
Use the B&N website on your PC to buy e-books using your old account, and download them from that account for use with Calibre.
This also has the advantage that all your B&N content will be still available in the B&N cloud to download new copies if needed.
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