I know this doesn't address the original question, but I'm a little confused as to the purpose of putting thousands of books on your Nook.
I usually keep ten or less on my Nook (in addition to my magazine subscriptions). I only read one book at a time and then move to the next in the series or whatever when I'm done with that one. I keep all my books in Calibre as well where I can easily sort through them. I'm usually never more than a day or two away from my computer, so transferring books is not a problem.
Other than bragging about carrying around your whole library, is there really any point to it?