Hi Briz,
I think I would have to preface my reply with this: no one knows what LDN does in thyroid autoimmune disease. There have been no clinical trials to assess the validity of LDN in thyroid disease. However, one can extrapolate from its successful use in other autoimmune diseases that it has the potential to mitigate the production of autoantibodies. You can take a look at the Survey results here at this site to see how others who have autoimmune thyroid disease are doing on LDN.
Some people who are taking LDN do see a lowering of antibodies (including TPOAb). It's difficult to know whether LDN has anything to do with a rise in your TPOAb or not -- it should have the opposite effect. LDN is supposed to modulate lymphocyte and cytokine imbalances and thus reduce autoantibodies.
Your antibody levels could also be due to stress, improper medication dosing (using ATDs), improper thyroid hormone levels, diet, and a whole host of other things. Increases in antibody production can cause fatigue, but so can endocrine imbalances (deficiency in thyroid hormone or even excess thyroid hormone).
I would want to know what your Free T3, Free T4 and TSH have been from the time you started LDN to now and what kind of ATD changes you've gone through as well. By the way, one can have a calm thyroid gland or silent thyroiditis while still in the throes of autoimmunity, i.e. antibody activity and infiltrative lymphocytes.
As for your last question, the problem lies with an immune system which produces and instructs antibodies to attack TSH-Receptors (in Graves' disease). Flu-like symptoms are actually from the immune system reacting to foreign invaders, but in autoimmune disease, the immune system is producing excess antibodies programmed to attack healthy tissue, making us feel unwell and often compromising our quality of life. The long-term goal is to heal the immune system while stabilizing thyroid hormone levels, and so it's understandable why you started LDN or are willing to be an explorer to help yourself.
BTW, you can ask Elaine what she thinks at her Q&A.
Valerie