wallybird7;
They went dead on into a thunderstorm.
What's your definition of a thunderstorm? There was no lightning reported by other flights or observed by satellite.
We don't know exactly, but the evidence presented so far doesn't point at that. They were using the radar to select a path between Cb's and became victim (or the pitots did) to the latent heat content in the out-flowing and sinking air from nearby towering Cb's.
Has anyone ever been trained for stall recovery in a deep stall?
Stall Warnings are provided and the training given is for procedures to be used to avoid stalling. Air Transport aircraft are not designed for, nor is their ultimate performance in a stall known, and therefore avoidance is the appropriate training.
Remember, this aircraft was lost because the correct procedure of pitch and power was not used when unreliable airspeed data became an issue. Becoming stalled was a by-product of that, and the logic associated with "how" and "why" this happened is really the issue.