Cheap little book written by Hanson. It's call Play Big. Great read for a teenager. I gave it to my son entering his freshman year and he used the tools from the book when he was at the plate and on the mound. Won the starting catcher's job as a frosh and the coach wanted all of the other players to use his approach when getting in the box. When I told the coach why h does what he does, he went out and bought 15 copies of he book and shares is each year with his players. Hanson has worked with major leaguers who have developed the "yips". He works with golfers as well.
The issue here is that results are not meeting expectations and the more he fails the more he stresses about each throw. My experience is that this is a mechanical issue that then turns itself into a mental one.
My advice depends on where the kid is in the cycle and that is only going to come from the kid being honest with you. If he doesn't know what's wrong but stays mentally positive look for mechanic signs of the balk being driven into the dirt. Short stride, late release. Etc.
That said it sounds to me like he is in the mental stage of this since it works when there is no batter and falls apart once the real thing starts. The key to curing this stage is to eliminate the expectations of results. He executes when nothing is on the line but once the expectation of results present themselves fear of failure steps in and prevents proper execution. You have to do something with him where he mentally says "well if this doesn't work who cares because it's not normal." To use a different sport analogy, i have a friend who had the putting yips when putting right handed. Turned him around and told him to put left handed and the yips disappeared. I've seen guys with chipping yips start chipping one handed. The limited expectations of doing something you haven't practiced frees u up from the mental expectations.
I would try something new with him. Teach him to throw a cutter, change his windup to include a hitch do something to make him uncomfortable with the process. If it feels weird and he's never done it before he won't have the expectation of perfection or the fear of dailure. You will have freed him up to be an athlete again.
Last point, The road out of the yips is a long process. If you find a solution that works stick with it longer than you would think to. He needs a sustained period of mental success before attempting to revert to normal.
But here's what I think, assuming it is not an arm problem but rather just in his head. I think if you try too hard to "hit the target" right on the button, you can sort of aim the ball instead of just throwing. You end up pulling the string a bit on each pitch, which can really throw you off. I think it is more of a problem for guys who are not power pitchers, who know that location is really important for them, and who therefore try really hard to hit their target. The further off you get with each pitch, the harder you try to "aim" for the target you are trying to hit, and it just gets worse as you become a head case.
If it were me, I would experiment as follows. Instead of trying harder to hit the target, in my mind I would try to throw "through" the catcher. In other words, instead of trying to hit a particular spot, I would imagine that the catcher is really two feet beyond where he really is, and try throwing through where he really is to reach a destination two feet beyond where he really is. I think that might keep me from pulling the string on the pitch to try and hit a particular spot.
If that didn't work, I'd probably shoot myself.
I understand you said his warm-up pitches are good but they are more than likely not at 100%. He may have an arm issue, especially after pitching the innings you mention.
Aside from an arm injury, I would take him on the side and cover up the plate so his primary focus is on the mitt. In college we always warmed up with the mitt about 6 inches off the plate inside/outside and worked our way in. Taught you to pitch to the mitt and not worry about the batter.