Hi,
I think arachdinoic acid is more of a problem in red meat than collagen. Arachdinoic acid promotes inflammation and can worsen or connective tissue disorders.
In Hashimoto's thyroiditis thyroid antibody levels are typically very high, much higher than levels in Graves' disease. Thyroglobulin antibodies contribute to thryoid cell destruction, and TPO antibodies are markers of inflammation, which also cause thyroid inflammation to persist.
If you initially had high levels and they rose dramatically after starting collagen, you might be concerned. But without having evidence of this, I don't think I'd stop collagen if it's offering physical benefits.
You might consider taking selenium (200 mcg daily) to help lower TP) antibodies. Avoiding excess dietary iodine, aspartame, known or suspected allergens, and cigarette smoke can also help.
Best, Elaine