According to wikipedia
Hashimoto's thyroiditis or chronic lymphocytic thyroiditis is an autoimmune disease in which the thyroid gland is attacked by a variety of cell- and antibody-mediated immune processes. It was the first disease to be recognized as an autoimmune disease.[1] It was first described by the Japanese specialist Hakaru Hashimoto in Germany in 1912.
en.wikipedia.org/wiki/Hashimoto's_thyroiditis
It would appear tp be caused by abnormalities in genes -
MMS works on pathogens in the body - bacteria, viruses, heavy metals, etc. Unless there are pathogens that are affecting genetic expression, (which I guess is possible, they've discovered in the last 10 years or so a lot more in the field of epigenetics) - I'm guessing that Hashimoto will not be affected (or may only slighly be affected) by MMS. It would be worth a round of protocol 1000 to see if there's inflammation or something that remits - I'm sorry.