It sounds like wapitibob has figured out the OP's question. However, I would think that they would give that permit to the applicant with the highest number of bonus points, regardless of whether that person is a R or NR. I don't think it matters that the person that originally drew the tag was a NR, since it the bonus round rule is worded "up to" the specific percent. Since the one bonus round permit was never guaranteed to go to a NR, it just did since a NR had the highest number of points, it should go to the next person with the highest number of points regardless of residency status.
With regard to TomHarveyB's question, there is one other thing to point-out. While the answer given to you is correct, I wanted to point out that it is completely possible for a person to draw their second choice in the bonus round and then at the end of the drawing there could actually be leftover tags for that hunter's first choice. In other words, it's possible to draw your second choice and G&F could have leftover permits in your first choice unit. While that's pretty unlikely for elk, since there are few leftover tags, it happens all the time in species like javelina and deer that have good numbers of leftover tags.
It's also completely possible to draw your second choice and never have even been given the chance to draw your first choice, which is likely what happened in the situation you mention. If your second choice takes fewer bp's to receive a bonus round permit than your first choice, and if you have the number of points needed to be guaranteed your second choice, they don't even consider your first choice.