WOW, cool robots. 
Is your pain skin set to invisible? Then visible when it takes damage. Do you endObject on the original mesh? Or just set it to invisible? How do YOU make it work?
Off topic, how did you get the spawning ragdolls to work? Is it a special build of blender?
Iād like to know the answer also. I oversimplify everything, I keep ragdolls on an inactive layer, end object on the original mesh, spawn ragdoll in itās place.
In that game I integrated the pain skin idea in to the level of detail script I wrote. Each body part is a separate object but all parented to the armature and rigged. When switching meshes for LOD or when taking damage I checked for critical damage and used the correct mesh as needed. In the end it wasnt a very good solution as it meant that both LOD and damage display scripts got called more often than needed.
For ragdolls, in the past I couldnāt get them to work with addObject as the rigid body constraints werenāt preserved when adding multiple objects, and if I added them all parented I couldnāt get them to go dynamic after unparenting them.
My rag-dolls werenāt built properly and didnāt work as well as some I have seen around here. But what I did , was to parent everything to a plane, then spawn the plane. (One object) The original enemy also had a plane that the armature was parented to, the centers being exact so the rag-doll would spawn exactly in the same place as the original. Mostly they fell apart, but it still looked ok. LOL
Not the best way, The spawn wasnāt very smooth. But it worked well enough for me.