Hi, Jeff. You'll probably get much better results posting this on the Pubit! Help Board. That's where the people who prepare ebooks for Nook publication hang out. Us folks up here are mainly just readers.
Just out of curiosity--What happens if you begin the highlighted portion with the word prior to the hyper-linked text? Can you then include the hyper-linked text as part of the highlighted portion (perhaps ending with the word after the link)?
If I am having problems highlighting specific words in an ebook, I don't worry so much about getting the specific beginning and ending words of a specific phrase as I do about marking the location of the information. After I've highlighted the location, not necessarily the specific words, I can add a note. I can search my notes to determine the location to which I want to return.
I don't recall ever trying to highlight hyper-linked text, but my immediate thought is why highlight and notate the link? If the (information in) the link is the part I want to revisit, why not highlight and notate the text of the endnote (the text I find by following the link)? Can't you highlight and add notes to endnote text?