If they kick him out of the program and it's because of missing work due to a disability, then that's discrimination on the part of the school. You could make a major stink, but obviously it's preferable to not have to go that route. I'm worried the teachers are going to become so irritated that they will play games--either they will make him out to be not as impaired as he is, so that he doesn't qualify for an IEP, or they will start depressing his grades and be really hard on him, so that they can kick him out. Only you know enough of the situation to say if any of those scenrios is possible, but that would be my fear. You have to make sure they follow the 504 because that is the only thing that is fair to your DS, but it may come with consequences. This is such a **** situation. No parent should have to spend all their time worrying about this stuff. If possible i would get it written directly into the 504 or possible IEP that he is not to be denied gifted services as a result of behaviors tied to the disability. His grades should not reflect late/missing work if the late/missing work is the result of 504 accommodations not being followed.
