Thank you for your question today, I look forward to assisting you. I have nearly 20 years of legal experience in various disciplines, including JAG.
Actually no, a general discharge will not effect his ability to receive ongoing treatment or disability payments if he rates those payments under the VA system.
It would deprive him of the GI Bill, but that is the only benefit lost between honorable and General.
If he has less than 6 years in the service, the command can initiate a discharge on the basis of performance or even alleged misconduct and push that paperwork through, without your son ever having the chance to fight before a board or court. It's called a "notice" discharge and his only recourse is to file a letter to the commander's making the decision. His CO doesn't have all the control, as it goes to the next level commanders for approval and review.
If those commanders agree, however, there is nothing he can do to stop it from happening. He will be forced, regrettably, to deal with the discharge after he is out, through the DD Form 293 discharge upgrade process. He would have to submit that form along with evidence of his medical condition, his previous exoneration at the court martial and his further evidence against whatever it is this CO is complaining about now, to the discharge upgrade board. He can submit that appeal to the discharge upgrade board for a period of up to 15 years following his discharge.