Surgery before Jr. year in D1 college, scholarship and school work

I believe there are 2  types of red shirt status: Medical  and hardship . Clearly, he will be a medical red shirt if he has surgery and is post surgery / rehab as a Junior . So, yes he gets another year of eligibility. But he can not play at all next year. Not one pitch or one AB.

Opinions will vary on the impact the injury will have on his scholarship. Essentially , an NCAA scholarship is renewable annually regardless of an injury or not. So, for example , if the player was healthy and played but in the coaches view didn't contribute enough or show enough potential to improve he indeed could lose his scholarship for the upcoming year. So that component already exists and needs to be considered .

With guys that are hurt and go through surgery most programs will honor the upcoming season. Or try to construct a financial package that includes other sources of money , Needs based or merit based aid packages to keep the player on campus and on the roster. As a rule MOST programs stick by guys that get hurt but there are clearly exceptions and hopefully we will see some other opinions here that can help you.

The easy part of your question is the eligibility.

"Redshirt," which is not an NCAA term, refers to a year that does not count as one of an athlete's four permitted seasons of competition. The medical hardship mentioned by strainedoblique is a provision that permits athletes who have season-ending injuries in the first half the season not to count that season as a season of competition if they haven't played in 30% of the team's games for the whole season.

If your cousin's son doesn't play at all next year, it won't count was one of his four seasons of play. If he comes back and plays at all, it would count as one of his seasons of play.

The hard part is what will happens to his baseball opportunity if he takes a leave of absence from school.

Coaches look forward, not backward. Except in very rare instances, such as encouraging a player to go to a JUCO to get more playing time, coaches assume players who leave school aren't coming back. It's extremely unlikely any coach would set aside scholarship money for an athlete who left the school and won't be ready to play in the spring if he does come back. That money will go to someone who will be there.

Maintaining relationships with coaches and teammates during rehab is extremely important. If the coach doesn't see day-in, day-out commitment to rehab and the team, your cousin's son will be out of sight and out of mind. 

Unless there are compelling circumstances requiring it, taking a semester off is a very bad idea if your cousin's son wants to play for his team again. From the coach's point of view, it signals lack of commitment to school and lack of commitment to the team.

Best wishes,

My son had surgery after his sophmore year at a D1 school. 

He had it at the end of May and was able to participate at the end of fall practice. He missed most of the fall. 

He attended classes and worked on his rehab. 

I guess I am not understanding why he would miss school?

As the others have stated. I haven't seen a case yet where injured teammates don't stay in school if they expect to be able to again contribute at said school.  As Swampboy stated:  injured guys need to be present and seen by the coaches to remain a part of their plans. 

Son had surgery (actually 2 surgeries) after Freshman year, with a 6 month PT and rehab program.  He went to school in the fall, hit some, and did get released to play in the final fall world series, but did not run at 100%.  He played full force in the spring so he didn't miss a season.  Scholarship stayed in force.

Yes dont understand why he would sit out Fall semester. Does coach/trainers know about his injury and needing surgery? U do rehab w trainers, school athletic PT, etc at D1 level if u have them. If injured playing school picks up what ins doesnt. You work together w school. 

What is injury?  He should be at school in Fall first for academic reasons and second to work w trainer and hang w team, show coach he wants to be there. Not sure what his reasons r for sitting out. What would he be doing in fall instead of going to school.