I would like to see some of his normal mechanics for comparison if that is possible.
Sometimes kids have a fear of hitting the batter. Rightfully, he doesn't want to hurt someone, so he doesn't throw as hard. Also, coaches may have informed him of rules that call for a pitcher to be removed from the game if he hits too many batters. He wants to play, so he doesn't want to risk not being able to pitch.
It's possible that, in the process of thinking this through, he's subconsciously changing his natural mechanics and may struggle a bit to find the zone. He has never thrown that way in practice--it's new!
Most kids will improve with more experience as they realize the batter will survive being hit with the ball and that batters have the ability to evade most inside pitches--if they choose to. There is nothing you can do about kids that don't have the coordination or reflexes to avoid being hit. You just have to feel sorry for them, hope they take to training and improve, or let them get Darwin'd out of playing the game.
To help him get over this, he can pitch BP to a few batters in practices, he can pitch his bullpens with a coach standing in the batter's box, he can throw bullpens with an infield screen in front of the batter's box while a kid stands protected behind it like he's going to swing. Any wild pitches will harmlessly hit the screen. (This is also a good way to train kids how to move to avoid being hit by a pitch.)
Eventually his confidence will grow and he will understand that every once in a while kids are going to get hit with pitches and most survive the experience.
I understand this completely. When I have to throw BP to a kid who can't protect himself at the plate, I change my delivery, slow down the pitches, and it takes me a few pitches to find the strike zone again. 90% of this game is half mental. The same percentage applies to the people as well. We can't get out of our own heads sometimes.