I have Hashimotos and have been on Tertroxin (Australian T3 med) and Thyro Gold NDT (previously on a different NDT) for several months now and have seen my anti-TPO and anti-Tg numbers skyrocket over this same period. In March my Anti-TG was 27.3 (reference is <4.1) and now it is 232. Similarly, my Anti-TPO went from 40.2 (reference is <5.6) to 376.
I haven't made any large dietary changes during that time (I still mostly stick to a gluten free and low dairy diet), and the only real change was that I began taking those medications listed above. My TSH has been supressed since March when I began taking them, and that would seem to go against the prevailing opinion among some here that a Hasimoto's antibody flare is impossible while the TSH is suppressed.
I have heard that NDT may cause an increase in autoimmune antibodies but I haven't really experienced it myself when I experimented last year for a short while with a few different brands of NDT. That would only leave the T3 medication as a possible culprit but I've haven't read anything that would indicate that line of argument.
I'd appreciate any feedback on this and if indeed T3 meds can cause a spike in autoimmune antibodies.
On a side note, this also explains why I've been needing to constantly increase both my T3 and NDT dosage over these past few months. I had assumed that I was becoming accustomed to the dose, but it's more likely that the increasing antibody attack on my thyroid meant that I was unable to naturally produce enough thyroid and needed to rely more on meds.