"Each student-athlete receiving athletically related financial aid earns one retention point for staying in school and one eligibility point for being academically eligible. A teams total points are divided by points possible and then multiplied by one thousand to equal the teams Academic Progress Rate score."
If a scholarship athlete goes on a mission, BYU loses the APR point for that student staying in school. It does not measure the length of time it takes a student to graduate, however. As long as the athlete stays in school and is academically eligible, the school gets the 2 APR points possible for that student.