For all NCAA divisions, a student-athlete is allowed at most 4 seasons of competition in each sport that he competes in, and a season of competition in one sport has no bearing on any other sport.
In addition, for D3 and D2, a student's eligibility for all sports is exhausted once the student has completed 10 full-time semesters. (D1 has a similar rule but it is 5 calendar years instead of 10 full-time semesters.)
The term redshirt doesn't really have a defined meaning. It is just shorthand which means that the athlete didn't compete and therefore didn't consume one of the allowed 4 seasons of competition. Not only did your friend redshirt in baseball, he presumably also redshirted in golf, track and field, and any other spring sport, because he didn't compete in those sports.
Normally, simply entering a single game triggers the consumption of one season, but if a player sustains a season-ending injury or illness in the first part of the season, he may be awarded an injury waiver. If the waiver is granted, then he is deemed to not have used a season of competition, in spite of having played in some games. Note however, that this waiver doesn't alter the 10 semester limit; it just wipes away the early season participation in games. If the season-ending injury happens before the player has appeared in any games, there is no need for the waiver.
But it is important that the player or college collect together the documentation which shows the severity of the injury, and a doctor's recommendation that the student should not compete. Such documentation could be used if a second season-ending injury or illness occurs. If that happens the player may be awarded a waiver to the 10 semester rule. It takes two seasons lost to injury/illness to get the waiver.
So, the coaches didn't need to communicate (the golf coach didn't need to know either
.) And, so far, your friend hasn't lost the opportunity to get in 4 seasons in each of basketball and baseball.
