The medical DQ is issued by DODMERB. It’s a DQ. Period.
Differing SA’s/ROTC’s (ie: USAFA and AFROTC, in your sons case) MAY decide to pursue a waiver. So in your case, USAFA has chosen to not pursue a waiver, to present. Which has no effect on whether AFROTC decides to pursue a waiver, or not. Both will be using the same DODMERB exam (DQ, in your sons case). Which, btw, is good for 2 yrs, with any updates since your exam date.
USAFA may not be offering your son an appointment, independent of the DQ. IDK, no clue. But the DQ may not have anything to do with not winning the slate or being appointed. Again, no idea. It’s easy to assume it’s the DQ that’s the reason, but may not be a factor at all in his appointment decision.
As far as ‘redoing the process’, he won’t do another DODMERB exam. What he has done is good for AFROTC as well. Be prepared to begin school still under waiver review. I believe it’s all automatic with AFROTC. But a waiver would be pursued should he accept the scholarship. We read every year where students are still under review (and no payment) for a bit at the beginning of school. Some waivers ultimately don’t come through, and then the student is faced with making choices about their school: namely, how to pay, or transferring to a more affordable option. NOT SAYING THIS WILL HAPPEN, but it does. Every year. And is the reason behind the standard advice to consider your school choice wisely (scholarships can also be lost….).