@ppst, hmm, tough question since we did not face the situation, the kid had 5s in all the 4 A.P.s she had by end of junior year, so we reported all (BCM and Micro Economics). So not sure what the ideal thing to do would be. But taking an AP course does not mean the AP exam has to be necessarily taken right? Some kids may simply want to do the AP course(s) to boost their weighted GPAs. So guess it may be ok to leave out the scores you are not happy with or not directly relevant to the intended major of study. But again, that is a guess.
Separately on a visit to RPI, the kid asked the admissions counselor what matters more, the school grade on the AP course or the score on the exam itself (since they have some pretty tough grading teachers in their school, sort of grade deflated school if you will). The counselor opined that the grade received in the school is more important since that shows the track record of the entire year and not how one performed in a 3 hour window of exam on a particular day. Also, I believe they have decent idea of easy grading vs. grade deflated and profiles of high schools in a given region.