If his high school does not use these credits to meet graduation requirements, and doesn’t list them on the high school transcript, that is OK. He will have to submit official copies of his records from both schools when he applies to college. What those places do to determine his overall GPA for admissions purposes is up to each of them. Some might only consider his regular school’s GPA. Some might re-calculate the overall GPA. Without contacting each place on his application list, you won’t have any way to know what they are likely to do.
Don’t worry about whether a grade will be weighted or not. Plenty of colleges and universities re-weight grades anyway. Worry about getting him healthy and through the coursework needed for graduation.