I used to be a power lifter years ago, then got really fat (around 400lbs. ) now I'm down to around 200lbs and wanna start hrt soon. Even though I lost a lot of muscle mass and strength already I still get back and hip pain from all of my muscle imbalances. I plan on starting yoga and piilaties classes soon to try and strengthen and lengthen my muscles and correct some the imbalances. But I was wondering if when you start hrt and your muscles start to shrink has this helped to relive pain from tight knotted muscles and over strained tendons.

If you are doing nothing to strengthen or build them then yes there will be a degree of muscle loss over time. How much though depends on genetics and other factors like diet. If you are doing pilates you'll find, just as genetic cis women who do it, you will strengthen your muscles but not necessarily bulk them up.