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Have you considered trying using Moon Reader? It's a free epub reader in the play store that's much better than the Nook app or Google books. Also I would try checking your books with the pc version of Nook to make sure they're not corrupted in any way.
I am having the same problem. I can transfer the files back to the galaxy tab but I can't open files from the sd card. My husband and I both have galaxy s2's where we access the files from sd cards and since the update neither will work.
The update to Marshmallow invalidates the previous folders used for sideloaded books on the tablet and on the SD card. You have to find the folder where your books are on your SD card, tap and hold until boxes come up beside the epubs, then click on the "more" tab and tap move. You then have to go to the following folder on your SD card -com.nook.app, then tap on the files sub folder, then tap done. Your books will then show in the nook library under " My Files" and you can open them.
If you sideload bòoks onto the main drive of the nook, they have to be moved to the NOOK folder.
I got this to work, but now a large percentage of my side loaded books are in the library, but won't open. And the ones that do open won't allow me to save progress. The booksmarks function does not work, etc. It varies from book to book. I've had to download a reading app, which defeats the purpose of even having a nook. My nook color though antiquated works better than this very expensive samsung. Anyone else having the same issues and a solution? Customer service has been absolutely no help at all.