typically each proprietary reader effectively hides the books you download internally in an effort to force user fidelity. Kindle eReader sticks theirs in \sd\Android\data\com.amazon.kindle\ and renames them with an alphanumeric code after splitting the cover and graphics to other files. I would expect Nook to do something similar and it may actually use the same folder paths with com.nook.books or some such. In any case, you can give a look with a File Manager app like ESFileManager.
Typically each app will allow you to download the generic form to your pc for the desktop version of the app sometimes...so perhaps you can try that to get a transferable copy.