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Try the Nookstudy program for your computer and see if it will allow you to transfer your notes, but I doubt it will let you transfer much of the highlighted stuff due to DRM issues.
What I do is use Calibre plugins to remove DRM, and then put the books in the Sony desktop software. This software will allow you to send your notes and highlights to a rtf file on your computer, which can then be printed out and saved for later reference. The Sony software is a bit buggy, but it is the best I have found for this purpose. Of course, you cannot use a nook with Sony software. You would have to buy a Sony reader or just read your books and do notation on your computer.
I don't know anything about rooting, but I do know the Sony reader for android is still in its infancy and not worth the bother.
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