I had terrible heartburn, just as you describe, when I got back
into being hypo, while in the
process of changing my meds. In
two days after starting on Armour, in order to increase my FT3 level, the heartburn was gone.
If you haven't been tested for FT3 and FT4 (not total T3 and total T4), then you should get that done. FT3 is the most important because it is the most active thyroid hormone. FT3 largely regulates metabolism and many other body functions.