If this happens after an unplug, try rebooting the Nook without doing anything else. It's actually put things back as expected for me. I leave my shelves as a list, and when I encounter the bug, the shelf will still show the correct number. Say it will show "5" when only 2 books are really visible.
Although if you pull the SD card for any reason from the nook, it will unshelve all the books that were on the SD card (the shelf count will go down), and you will have to reshelve them when you reinsert the card.
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