Sorry, I don't know what will happen. Just wanted to say good luck to you and your baby girl and I am praying for her.
I believe less than 5% of thyroid cysts and goiters are cancerous, ...that's what I was told by my dr and have read. So there's a small chance it could be. It could be from a virus she has recently had. As far as the hypothyroidism, that would be treated with taking a small dose of thyroid hormone and in most instances will correct the problem.
Prayers for her..and you!