You need to do a factory reset of your Nook and let the Nook reformat the sd card.
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I tried a factory reset, but something goes wrong when connecting to B&N for the deactivation. And when the deactivation goes wrong, the reset will not complete.
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You will probably need to change you B&N password. I had a similar issue with my Nook and my Linux P.C. ie it would not work with the Linux pc but would work with my windows 10 tab. It unregistered/deactivated ok but would not register until I change my password. It took two reset cycles to finally get it to work with the Linux pc
As a best practice I have found that putting the Nook to sleep before doing usb transfers seems work faster and better with less problems than leaving it awake.
luck
bernie