The calories sound lower than 1300 to be honest.
If she had been avoiding carbs (for how long has she been on low carbs?), the thyroid gland will slow down.
How long has she been eating such a low calorie consumption?
In all honesty, it may be that she has developed an eating disorder, and with that, her digestive system has backfired on her.
I am a natural BBer, but I do know that you need to eat enough calories, and a lot of good quality food, and a wide range of it to grow muscle and stay healthy. The same sort of things that apply to men making the most of a steroid cycle also apply to women, just that the drugs are different and a few more precautions.
There is a thread related to dieting and metabolic damage on this site as well:
http://www.elitefitness.com/forum/w...training/dieting-metabolic-damage-570773.html
I would recommeng getting Tom Venuto's burn the fat, feed the muscle.
There are some exerpts in this thread:
http://www.elitefitness.com/forum/w...-training/help-sort-out-your-diet-582178.html
It may be a good idea for her to take a break from cardio for a week or two, focus on weights
http://www.elitefitness.com/forum/w...ardio-queen-may-counterproductive-580116.html