You might want to move this over to hitting.
Perry Husband has a nice section on his web site that has keys to hitting and 5 minute fixes. I like to go back to it when my son struggles just as a recap I pasted the pop up part here. Rest is at:
www.hittingisaguess.com Frankly I have found that the only way my son could develop consistency is to have someone who REALLY knows a his swing work with him over a long time. When he gets in a funk we go see him and he immediately sees what he is doing wrong and fixes him up.
I know this really will not help you in this situation, but I would stongly urge him not to re-do the swing in season, this will make a bad situation worse. I suggest you continue to help him like you are try to find a small flaw right now. Maybe talk to his HS coach also so you are in sync.
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From Perry Husband:
5 Minute FixesPop- Ups - Almost all pop-ups are caused from the swing plane of the bat going up and by being late by about 3" or more. 4 Main Causes : (1) Grip - Make sure both hands are going the same direction. Get your grip and extend all the fingers of both hands, if they cross, they are going different directions and that will make the bat go 2 different directions. Adjust the hands so that the fingers of both hands are going the same direction. (2) Back side collapsing. The back knee or the back foot collapsing will cause you to swing up. Traditional thought was that the shoulder "dipping" caused the bat to go up. The shoulders are not at fault. The back side collapsing causes the shoulders to tilt upward and the bat follows the line of the shoulders. To fix that, push hard off the back foot and lock out the front side. This will make the swing line straighter and the pop-ups will go away. You will still hit the ball in the air, but it will be a harder hit flyball. (3) Hands too high in the finish. If you freeze in your finish position and check the hands, if they are above the shoulder line, the bat will have gone up as well. Finish with your hands lower. The list of old timers and new age hitters is long that finish with their hands low.