BYU has not been the same team since Max Hall left. The last AFA-BYU meeting was in 2010, and AFA won it 35-14.
AFA was terrible last year 2-10, so BYU probably would have won. They were 7-6 in 2011 and 6-7 in 2012, so BYU would have likely won those as well. BYU would have lost to AFA (8-3) this year, since they beat both Nevada and Boise State, teams that BYU lost to.