(((LovetheOcean)))
Let me see if I can help a bit!
One reason suggested for avoiding soy if one has an endometriosis diagnosis is that soy (and yams and black cohosh) contain plant estrogens. Those estrogens can fuel the endometriosis in some women. Additionally, if someone has an estrogen dominance issue, which many of us with endo have, the soy and other plant estrogens can increase those symptoms as well.
Since you are using estrogen replacement, using or not using soy isn't really an issue except that it could increase the amount of estrogen in your system. However, any estrogen, especially without progesterone or progestin, can cause any remaining endometriosis to grow and spread.
Why does your doctor feel that the endometriosis on your large intestine will dry up, especially if you are using ERT? Personally, I have never heard of the lack of cycling allowing endometriosis to dry up. In fact, there is research and studies indicating that unless endometriosis implants are removed, they can plump back up once estrogen is introduced.
From personal experience, endometriosis was left on my bowel walls. My GYN didn't think it would be a big issue. I did keep both of my ovaries so I had plenty of estrogen. However, that also meant I had progesterone, something you haven't indicated you are using. (Progesterone can be used to try to keep endo at bay.) The endo on my bowel walls did spread and also allowed for an adhesion between that endo and my vaginal cuff. It also allowed for IBS issues and symptoms that landed me in the office of a gastroenterologist and I had to undergo a lot of GI testing.
My best advice for you would be to get a second opinion regarding what would be best for you. Personally, I would avoid the soy to keep the estrogen level lower, but I would also be using progesterone along with the estrogen replacement. I would also find an endometriosis specialist and ask about the endometriosis that has been left behind. Find out from a specialist if that endo will dry up and if not, what your options are for either keeping it at bay or removing it.
If you have specific endometriosis questions, feel free to pop over to our Endometriosis Support forum!
Best wishes!

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