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Works for me. I'm using Calibre 2.59 on Ubuntu Linux 16.04.
Prior to the B&N update I did go to the "Configure NOOK" dialog and edit the "list of folders on the device to which to send ebooks", Mine reads thus:
NOOK/My Books, NOOK/My Files, NOOK, Calibre_Companion, Books, eBooks/import, eBooks, sdcard/ebooks
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