i dont know how to get rid of that but how did you sideload the books in the first place? I can't figure it out no matter what i try. I have drm free epubs on my mac and have no idea how to open them on the nook app on my n7.
I've noticed the same behavior on my device as well. The other weird thing is that if I delete one of the files one of the entries goes away but there's always one "book" left that doesn't have any cover art. It has to be caused by recent update, I don't recall seeing this behavior before. As soon as I finish the book I'm reading I might delete everything, uninstall the app and see if it's a weird caching issue.
And the way I loaded the files was to simply drag them to the My Documents folder under the Nook directory. No special apps needed, no emailing.
As a follow-up to this, after I finished the book I was reading I force stopped the app, cleared the cache and data and the duplicate books were gone. Of course, I had also gone through and renamed all the files on my device to remove all apostrophes, ampersands and exclamation points, so that may have also been a part of the solution.