Firstly, I think someone shared how to do this. I can't find the thread now.
All I could find was this that Laurieb wrote:
If you want a book totally archived, you have to do it from your library online. There still is an option to see which books are totally "archived", versus "moved" to the Nook Cloud. After opening your "Book" section, tap on the icon on the lower left hand corner that looks like bulleted lines.
I remember reading somewhere how to do it. Just can't remember right now.