OP- hugs. This is a challenging situation and I hope your son continues to mend every day.
If it were me- I’d start de-emphasizing the importance of AP’s, advanced level courses, “getting back on track” or any other messaging of that ilk.
College will always be there. I know it’s hard to think that way if your son is at a competitive HS where the top kids just sail away in a little boat from HS off to college without missing a beat- but trust me- college isn’t going away.
Focus on your son’s recovery, on his ability to make it through the school day without experiencing exhaustion or headaches or whatever other symptoms he’s had. If he’s not ready to apply to college his senior year- then great, he’ll get a job or do volunteer work and continue to recover. If he is ready to apply- great. Find a college which will meet your son’s learning needs at that moment- and if he needs something more challenging after a year there where he’s blown the cover off the ball- he can transfer.
I’d be exhausted if I were managing a kid’s recovery, plus doing battle with the school system and the bureaucracy, plus worrying about AP classes and college admissions. Focus on your son. If the district is mostly uncooperative about giving credits on the transcript for the outside stuff your son has done- might do-wants to do- well, is it really worth fighting that fight?
And it goes without saying- make sure your son gets an eye exam if he hasn’t had one recently. And since he’s seeing the neuro this week- ask about a thyroid check? Just get your ducks in a row in case there are other (easy to correct) things going on which have slowed down your son’s recovery.
Big hug to all of you.