So you want to take your character model (let's call it fileA) and reference it into a new scene (fileB) so you can rig it...That way, your buddy can refine the model while you work on the rig.
You turn to your buddy...
1) The set up:
fileA consists of a polyCylinder.
The cylinder's faces have been assigned different materials.
fileB contains the rig, and a reference of fileA.
fileA:polyCylinder has been bound to a simple skeleton.
2) The problem:
When you modify the material assignment in fileA, you expect the changes to be visible once you reload the reference in fileB.
However, as you can see, the modifications are not apparent in fileB.
3) The issue:
It follows that since you reference the contents of fileA into fileB, you are working with the same object.
That's true up until you add a deformer. Once you do so, Maya updates the DG to look like this:
fileA:polyCylinderShape > skinCluster > polyCylinderShapeDeformed
..where the referenced node fileA:polyCylinderShape has become an intermediate node.
I'd like you to select the fileA:polyCylinderShape node and, in the Object Display tab of the AE, turn off the Intermediate Object attribute. The shape will appear in the viewport and you'll see that the correct material assignments reflect the changes you made to fileA.
To resolve the problem, we have to somehow share the shading group sets between the fileA:polyCylinderShape and the visible polyCylinderShapeDeformed nodes.
If the material assignment had been made on a per object basis, this would not be a problem, since both our shape nodes share the same transform. In this case, however, the material assignment has been made at the component (face) level, and the problem is that the shading group sets connected to fileA:pCylinderShape don't automatically get connected to the polyCylinderShapeDeformed node.
4) The solution:
To pass the connections across, we'll use the MEL script deformerAfterObjectSetMod (sourceShape, destShape), like this:
Use the MEL deformerAfterObjectSetMod to share shading group sets.
You'll have to use this workaround everytime you reload the reference file after making a change. I recommend saving the command to a shelf button. Or have it execute as a script node when you open the scene.
Thanks to Ray and Sivanny for their input.