If you have overgrowth of endometrial tissue, that will have more to do with your odd menstrual issues than the
synthroid, The Medroxyprogesterone is not a double whammy with the
synthroid because synthroid is a thyroid hormone and progesterone is reproductive hormone - while all hormones must work together in the body, they each have a different function.
Typically, side effects from Synthroid only last until your body has adjusted to having the hormones it's been doing without.