Your period will stop with either low or high body fat. It is a physiological survival mechanism.
When menstruation ceases due to body weight it is called "amenorrhea".

Basically it is the body shutting down non-essential systems for survival, a "you can't support life at the moment, your body is in alert mode" kind of thing.

I would tell her to ease off the gym a little and work on maintaining weight and make sure not lose any more.

There are some essential oil blends that she can use to stimulate her menstrual cycles again though that work well.