I am almost positive that the OP is AFROTC.
I want to say because this was a DoDMERB and AFROTC waiver issue, you might be okay. They may have held it awaiting the outcome of the waiver.
Here is the other problem you might not be prepared for...dealing with DFAS. As an IS recipient you may also be entitled to 6 months of the stipend you did not receive and the book allowance. That is a whole new ball of wax, one that takes sheer determination to fight for it.
However, they may also say as Clarkson illustrated...you did not contract, thus the money was put back in the pot. The reason why I say this is because on another thread you only registered for C200 in the past few days. They may have assumed you quit AFROTC because of the medical issue, thus revoking the scholarship.
You need to contact the NCO again. If he/she doesn't have the answer, than speak to your DO. Work the chain of command. Give them a few days to get back to you. I bet dollars for donuts they will get back to you, it may take a few days, a couple of gentle email reminders, but they won't forget about you.
Good Luck. AIM HIGH ABOVE ALL!