I think some people have had success using the Calibre software. Perhaps they will comment here.
My experience was that any time I side-loaded a new book to the NOOK GL3, any shelves I had created from the ereader screen would disappear. This happened to shelves that contained ONLY side-loaded books. Any shelves that had at least one book from the B&N store survived, but all the side-loaded books disappeared from those shelves. Very frustrating.
To be clear, the side-loaded books were still on the NOOK, perfectly readable. But the shelves were nearly unusable.
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