Your situation is a perfect example of why it is so important to remove ALL the endo, no matter where it is. When endo is left behind, by accident or on purpose, the pain and problems can continue. She has been taken off her estrogen patch. Yours is a troublesome problem. If her ovaries are out, your wife needs estrogen to protect her heart and her bones.
Endometriosis can be horribly painful, but osteoporosis and heart disease can be deadly .
The CEC approach would be to surgically remove all endometriosis. It is likely your wife has adhesions, too, and they can be removed at the same time. When all the endo is gone, there is nothing to fear from estrogen. Many women have been told that it is impossible to have endometriosis after their reproductive organs have been removed, but this is not the case. We stop having endo when the endo is removed.