Here's my understanding, based on
this synopsis. Anyone more knowledgeable, please feel free to correct.
In calculating APR, each scholarship player can earn up to four points: one for being academcially eligible each semester, one for staying enrolled each semester. The APR is 1,000 multiplied by (the number of points earned by the team divided by the maximum number of points earned by the team).
I think that means that an 11-man Syracuse roster could earn as many as 44 points for an academic year. If two players leave school prior to graduation (by withdrawal or transfer), they would each forfeit the point for staying enrolled. If they're academically eligible when they leave, each earns the other point for eligibility. If they aren't eligible when they leave (because of missed classes or neglected coursework during that term), they don't get either point.
The system is set up to minimize penalties for teams whose players leave early but are eligible when they leave; they're only penalized half as much as they would be under a review of graduation rates, which many coaches claimed was unfair.