Not that an appointment should disqualify him and he should definitely keep banging on doors to find out why that happened, but maybe they know something you don't yet and an appointment is on it's way? Silver lining
But an appointment to a SA should not disqualify someone from a ROTC scholarship. Reporting to a SA disqualifies someone. It is quite possible that someone would prefer a Civilian College and ROTC over a SA. Acceptance of another ROTC scholarship should not disqualify. There have been many with AROTC, NROTC and AFROTC scholarships, none active, but they are choosing which is right for them. Maybe they think he is in a SA or has recieved scholarship money from another ROTC program. I would be knocking on doors to find out the specifics, because it doesn't sound right. Maybe they have him confused with someone else.