Okay let me see if I get this straight.
Your adrenals are dead and she is giving you progesterone to fix it? Ummm.. DUH? NOT a good idea. If she wants to start lower on the synthetic food chain for the adrenals pregnenolone is where it is at... however you need a COMPLETE adrenal work up.
This is a full ACTH stimulation test evaluating ACTH, Cortisol, Aldosterone, renin, progesterone, estrodoil, cortisol, DHEA and pregnenolone. There may be a conversion issue in your adrenals that is genetic and has been triggered by your thyroid dysfunction. This is what happened to me. My adrenals are not dead.. exactly.. they have just shut down the cortisol and aldosterone manufacuting lines. Everything is getting shunted to DHEA, testosterone, and estrogen.. mean while I suffer from adrenal insufficiency because I can not convert my pregnenolone into cortisol, cortisone, or aldosterone. The only solution for me is to supplement my cortisol and aldosterone and thus cause my ACTH to fall to normal levels.. cutting back on my abnormally high levels of DHEA, Estrogen, and testosterone. Talk about a mood witch.. that is my middle name.
Progesterone can be shunted to DHEA.. or converted into cortisol and aldosterone.. taking it may or may not improve your issues.
So what are your lab finding and levels? Also why have they not tried a combination of Synthroid and your natural T4/T3 supplement? What were your last Ft3 and Ft4 levels? In the cause of adrenal issue they interfere with your T3 conversion.. making you have too little when cortisol is high.. and too much when cortisol is low. Since you indicate that you have high cortisol in the morning and low in the evening.. you may only need to take your T3 in the morning. Versus twice a day as most T3 regime recommend. All in all you are on the hormonal roller coaster. You are not alone.. I ride in the last car and get jerked around a lot. My body wouldn't have it any other way.
It took 5 months to get my cortisol levels stable.. but I was not dealing with fluxing, I was dealing with dead cortisol production. It is possible, but it takes aggressive hands on testing and management. I am continually fighting the mineral electrolyte balance game.. right now I am low in potassium.. that SUCKS big time. But I am almost there with regards to cortisol, aldosterone, and Ft4 and Ft3 levels. My latest journey is to determine if my adrenal and thyroid issues have caused me to manifest insulin resistance and PCOS.
My medical history list is getting crowded. All in all when things are out of whack you need regular routine testing.. every 4-8 weeks.. with my adrenal mess I was in every 5 weeks for testing. I am fighting a constant battle to get and keep my B12 and vit D levels up in normal range. My Ferritin is good and my Ca is trying to fall out of normal range on me. The key is not to give up. I suspect that you are out of balance on your Ft3 and Ft4 levels and that you need additional support on the adrenals... but what you need is going to take time and systematic tweaking.
For many of the adrenal tests to be true you may need to go off of your beta blockers and supplements for at least 2 weeks. You also have to ditch taking hormonal supplements containing estrogen and progesterone. If you take estrogen and progesterone.. these will interfere with your blood work.. making them artificially high.
I am sorry that I do not have a simple answer.. but when dealing with the endocrine system.. simple would be miracle. Are you taking DHEA by chance? What are you taking medicine and supplement wise.. list everything. It can make a difference.