When I started running, I couldn't make it three city blocks without an asthma attack and cramps. Now I do 3-5 miles of hill running per day in the country summer sun. (Tennessee)
Over the past few years I have been developing a system based on incremental flow, as you mentioned. You can absolutely use small habits, and also leverage the Flow State proper in order to train. Eventually you are able to graduate to multiple spinning plates. (to reference your other comment). As you say the greatest danger is dropping all the plates in the presence of a minor stressor since you are operating at your current capacity.
What you end up needing to train is getting back on the horse. It's similar to the notion of "Returning to Breath" in a meditation practice. I have a leveling system and an economy built in, so that I gamify the practice of picking up the pieces. I'm currently working on smoothing out the difficulty curve, comparing several game mechanics like leveling down, adaptive difficulty, and triggering special modes. The idea is to have some sort of a pressure relief valve built into your life.
Do you use any systems in your own life?