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This happened to me when I updated the Comixology and DC Comics apps. The only way I could find to get the duplicate app icons to go away was to edit my profile info so that the original versions of the apps were disabled. Under the Edit Profile settings, there were two apps showing, one was the earlier version and one was the updated version. Luckily the new updated versions had new icons so it was easy to tell which ones I had to disable.
I have this problem now as well with Netflix. Thanks for the workaround but I sure hope B&N does something to fix this.