FYI I had this problem too. It was easily rectified (once I figured it out) by using android file transfer app to edit the names of the books. Apparently Nook doesn't like apostrophes in the titles. Once I deleted all the punctuation in the book names they instantly appeared on my Nook. And it doesn't change the names of the books on your Nook, so you don't have to be annoyed by misspelled words.
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