I created a books subfolder in the Nook folder. I put one ePub in the books subfolder and one directly in the Nook folder. The Nook picked up both. Then I created a My Documents folder which was not a subfolder of the Nook folder. The Nook did not see the book in that folder.
So, if you want a My Documents folder, it needs to be a subfolder of the Nook folder for the Nook to see the books.
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