Shoeless: I went back and checked the chronology of my son's paperwork and saw we got the financial aid letter on April 1 with no mention of any NROTC scholarship. What I recall was we called the Financial Aid Office and discussed the process with them. In our case, we didn't even get a late fee - the school was on notice via the NROTC unit and got their payment soon after school started and DS passed his PFT (orientation). In a sense, it was a no-brainer.
In reflecting on this comment from you post, I would offer the following: Your DS isn't the first and won't be the last in this situation. The school is used to dealing with ROTC students and has a process in place. The NROTC unit at the school is also used to dealing with this. It will all work out.
Congratulations to your DS.