What are you tying to figure out? She lost her breasts because if you are already thin and you try to lose bodyfat thats one of the places it usually comes of sadly.
If she is that active she needs to be eating at least 6 protein heavy meals a day. Her body has probably went in a starvation mode and is holding on to the last of her bodyfat.
However it sounds to me like she has body dysmorphia and an unhealthy outlook on her body. At 16 and for her height and weight she sounds like she looks great.