I agree with the above post. I lost both senate seats, but because I already had a Presidential as well as ROTC nomination, West Point placed me on the national waiting list. Holding a congressional nomination is an incredibly less competetive position to be in. So as long as he gets the congressional nom, I should think that he has a good chance of gaining an appointment because he is already found by the board to be fully qualified for admission.
You only compete with other candidates who have the exact nomination as you, so when you hold only a presidential or ROTC nomination, you are competing with literally hundreds of other candidates. Once you gain a congressional nomination, your competition lessens to no more than 10 candidates. This is because each state representative is in his or her own nominating category. So a candidate holding a nomination from David Scott, which is in the GA-13 category (Georgia-13th voting district) will not compete with any candidates but the other GA-13 nominations. Each congressman can only have 10 attending one academy at a time, so it would be easy to assume that there are usually no more that 6 or 7 nominations from one congressman to one academy per year.
That said, the senators and your son's congressman do talk to eachother to ensure that they do not give three nominations to the same person. I was denied by both senators within a week of submitting my applications. on 21 NOV of this year I gained my congressman's nomination, and on 15 DEC I gained the appointment to USMA. If your son gains the congressional nom, I would say that he has more than just a hope of an appointment, given the fact that he is already fully qualified for the academy.