As we all know, not everything on the coaching side is black and white, cut and dry. Every situation needs to be looked at and handled on an individual basis in some instances. With this particular kid, since he was the only one who did not stay, I feel you and/or HC need to have a sit down talk with him. Ask him why he left (albeit optional). Maybe get him talking and he will reveal something interesting you may not have previously known? Home problems? GF problems? Health issues? No food to eat? Seriously! In having an honest heart-to-heart with him may completely change everything. Then again, it may reveal true character as well.
A couple of years ago I had a player, a very talented player at that, who should have been on the V but made JV both his Soph and Jr years. He would maybe/maybe not show up to practices. During games, he would maybe/maybe not have his cap, spikes, etc... Dad was so gung ho about him playing and always told us coaches that we need to find more motivational factors for kid (as that was what dad said he was trying to do as well). One day, after many motivational speeches from all the coaches, me and another coach decided to have an honest heart-to-heart. We told the player that nothing that was being said would leave the dugout. We made an emotional break through with him and he finally told us that playing baseball wasn't his dream, yet it was his father's dream for him. He and his father's relationship was fractured due to this reality. He understood that he was good, and admitted that he could have actually been better if his heart was in it. I suggested that he found a time to express these exact feeling to his father, and they could process it together and hopefully come to an honest, peaceful conclusion. Player reluctantly finished his Jr. season and had that talk with father. He did not play his Sr. season. He and father came to an agreement to where son would work on academics.
With all that being said, these type stories are a dime a dozen. Find out directly from your player what exactly is going on in his world...