I accidentally overwatered my sunchokes, and they started turning red, so now I'm watching them heal back to a very healthy plant. What part of them heals last?
The plant heals as a whole. If your overwatering caused any root rot, and the plant recovers, It will usually wither somewhat at the initial damage, and perhaps lose some growth on the extremities, but then perk up and begin growing again. Not usually accompanies with a change of color.
If there was no rot, and the only damage was through oxygen deprivation (which also stops the microorganisms which are making nutrient exchanges with the plant) growth will slow down, and you are likely to have a less concentrated chlorophyll (which is why colors like purple or red sometimes show). This slows growth way down, and in extreme cases the plant can die. That is only caused by nutrient deprivation and will stop as soon as the soil dries enough to become active.