Soya, like brassica vegetables (eg cabbage) is a goitrogen. It stops the body absorbing iodine, and iodine is needed to make thyroid hormone, thyroxin. So if the medicine is to help the body make or convert thyroid hormones, you would not want to limit your iodine uptake. (If the medicine is actually artificial thyroxin, not sure what the link would be)
BTW, cooking brassicas s thought to inactivate the goitrogen. Again, I'm not sure about soya.