This is a bit misleading - the APR is often stated as a number but is essentially a percentage... i.e., (numerator divided by denominator)... if a player is 'run off', but is in good academic standing, then transfers to another school.. (or if a player goes early to the NBA, but leaves in good academic standing), there is no increase to the denominator (i.e., the result of which would be to lower the APR).
The issue is usually kids leaving early for the NBA or quitting school. See: Syracuse a few years ago. Sometimes, during the second semester when a kid is going to go pro, they say, 'forget school'. That is where there can be real damage to the APR. But if your APR is otherwise 1000, and four kids leave early for the NBA, but all leave in good academic standing, your APR is still going to be 1000.
Likewise, if you 'run off' a kid, saying, 'hey, you should go to a different school where you might get some PT... it's not going to work out here for you'... that is not going to cause your denominator to increase unless the kid isn't in good academic standing.