My DD is still pending with three nomination sources. She’s not too worried because of plan B and also knowing my backstory with USNA.
The SA’s are not necessarily looking for someone perfect in every way. I know this because I was one of them. I was accepted to NAPS (this was 25 years ago) with an F, a couple of D's (in physics), C's and B's, and a few A's on my HS transcript. But I was stellar at taking standardized tests. I had a story of overcoming huge life obstacles in my freshman and sophomore years of HS and had fixed my life by the time I was a senior (team captain, class president, and other things). I also know that several of the USMA cadets that I taught also had life stories that were less than perfect--one is right down the road from me right now, doing a great job in the Army. The academies are looking for someone who will make a good officer, not necessarily a perfect person. I had a slight amount of insight into USMA’s process back when I taught there (10 years ago) and was calling candidates, but I am sure it has changed since then. In fact, some of my cadets who had the hardest time adjusting to their plebe year were the brightest because they had issues working with cadets who were not as astute as them. You work with people of all levels of knowledge and insight daily in the military.
I will also put this out there: I know where a few of my USMA cadets were in a "this is the only way I can go to college" situation—again, backstories matter. Those were possibly the most motivated cadets in my class, even though most of them struggled to pass (because some had never had chemistry before).
To close out my own story, I went to NAPS, decided it was not for me, left, did Army ROTC, was an Apache pilot with a fantastic career (probably better than I would have had in the Navy), and am now retired (w/three degrees financed by the govt), so no it's not the end of the world that you (or your child) is not going to an academy, have them continue to do their best and reapply or commission through ROTC or OCS.