Graduation rates for ncaa athletes are only counted for players receiving athletic scholarship money.
Students are scored one point for being eligible and one point for returning to school each semester or 4 points per year.
If a player leaves after their junior year but was eligible, the team loses a few points which goes into a somewhat archaic calculation. The NCAA has noted that it would take several players leaving for the draft or any reason before a team had their APR score drop dramatically. In the long run, it won't be the players that leave that hurt the APR score but the players that stay that are not eligible or the players that neither get drafted but leave anyway and were not eligible as that could be a 2 to 4 point deduction.
The emphasis will have to be on recruiting student-athletes that are interested in staying at least 3 years and are interested in doing some work and being eligible.
As far as the reducution of scholarships is concerned - If you are banking on your son receiving a significant athletic scholarship for baseball, I would suggest you not hope too much. There are 285 D1 baseball programs, but many of those will not be fully funded anyway. I know plenty of programs with 1,2,3 or maybe 4 scholarships to offer for the entire team. Many of those will also be state school programs where a full scholarship might be 10 or 15 thousand dollars. Removing one of those scholarships because of a low APR might mean a 1 to 2 thousand dollar hit to a few players. Hardly chump change, but in the grand cost of some colleges, not a huge loss either.
Unless you are a top player, there is far more money available in academic scholarships and grants. I spoke at a school this week and invited a D2 coach down and he said any student applying early action to his school that has a 3.0 GPA and SAT of 1100 automatically gets $11,000 in aid, 3.0 1200 SAT gets $12,000 in aid and 3.0 1300 SAT gets $15,000 in aid. Thats before admissions has even sniffed your financial aid application or looked at your EFC. If you would like to divide 11.7 scholarships into 30+ baseball players on a team if you happen to be recruited by a program with 11.7 baseball scholarships, you are going to get a 33% scholarship perhaps, and anyone that gets 66% means another player gets 0%