Francis,
I think this happens at all levels, not just D1. Coaches job is to get the best talent possible through admissions and onto the baseball field. I've seen this situation play out especially after injuries. Guys lose practice and playing time and it is difficult to win that position back because the player doesn't have the reps.
What I find interesting about your story is that he was a part-time reserve his senior year. This tells me his skillset was limiting, as they didn't consider him for another position in the lineup or value his bat enough to get him in the lineup.
It happens.