From the details you have provided; you have hypothyroidism and on Eltroxin as replacement. Your bones can be affected only if you are over treated. Over treatment can be detected by TSH. If TSH is low, it means over treatment and you need to reduce the dose. If TSh is in normal range then dose is fine. There is direct involvement of bone in the other type of thyroid disease called as hyperthyroidism, and can lead to osteoporosis but with treatment this is reversible. This disease is opposite to hypothyroidism in which there is reduced (hypo) function of thyroid gland.