I'm still amenorrheic as well after losing 40-something pounds and I'm at a perfectly normal weight (5'4, 122-125). Mine is most likely due to overexercise and underfueling - I've corrected that situation and it's still not back /sigh. I'm at 2K+ calories a day and a reasonable amount of cardio/weights. Thyroid is fine, other things fine. It's been over 6 months .
My MD thinks it will just take time for the body to kick back in to producing the proper hormones. BC Pills are an option, but I'm 37 and I'd prefer not to take em if I don't have to.
FWIW, it's not related to low carb - I followed a much higher carb plan, very similar to BFL and in maintenance I'm eating carbs at each and every meal.