Flares have been handy (although unwelcome) for me.

Once I am not in a flare and one comes, I then examine what has changed in my life. New shoes, over-exertion, re-introduction of a food, virus infection etc. This is how I isolated potatoes and how they can cause burning for me, as well as MSG.

I do think autoimmune flares would be harder to detect. They might come up after a flu shot or some other invasive situation.
But they may seem more random in general.

I will say my new Dr. Scholl's memory foam slip ons have been great. I am having much less foot pain/discomfort at night on the days I wear them alot around the house.