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I use calibre to orgnize ebooks and sideload content onto my Nook. I cancelled a job while calibre was uploading books to the Nook in spite of the "may corrupt" the device warning and from that point on the "my documents" section of my Nook was wacky. Sometimes old content that I'd taken off would show up, randomly only '.jpg' images (calibre generated covers) would transfer instead of the ebook, it would take forever for things to load, it would say I had 40 files but only show a dozen, etc. etc. etc.
I didn't try the 'reset' options above but the manual restore worked perfect and now everything is back to normal.