How are your ebooks already listed on B&N? If you went through a publisher like Smashwords, you’ll have to go through your publisher in order to have them removed from the site, more than likely, just like they were print books and you were moving from one publisher to another. As long as you retained your copyrights, you can then load your own data through the pubit platform.
You definitely don’t want to have two of the same ebooks on the website – this is confusing for customers. I’m a customer and this would confuse me. Plus you get a 50/50 shot of sharing your royalties with your publisher. It sounds like it may take a little time for it to all happen, especially going through your publisher, so patience will be a virtue, and once the first set of ebooks are off, you could load the second, identical set.