Have you tried moving one of your ebooks that contain notes over to your PC and looking at the ebook in Nook for PC (a free program you can download from B&N)? If you did that, and the notes were still there (on the PC), there might be something you could do on the PC to capture those notes, because of the PC platform is MUCH more flexible. I don't mean that Nook for PC is more flexible, but the platform itself is. For example, the notes may reside in another file that you could access, or if they are inside the epub, you could probably pull them out using Sigil.
Edit: if these books are ones you purchased, you'd have trouble with the Digital Rights Management (DRM), so in order to really manipulate the files, you might have to remove the DRM too. This is a whole other issue. But for starters, try seeing if the notes are still there after moving the book to the PC.
Last edited by RAH; 10-20-2012 at 08:28 AM.