Hello blueduck!
Seems you want to add a material to a model. To have that done without problems as those you described, I use following procedure:
1. export the model with the original material
2. replace the linked material by the desired 2nd one
3. export again the model but make sure with a different name (add something such as _2nd_mat)
4. import the *.obj into the 3D editor, delete the 3D object (the material, however, remains)
5. import the *_2nd_mat.obj and you have the two material, both with the correct ID
6. start re-mapping or whatsoever
There might be easier and more sophisticated pathways but this one works smoothly with Wings3D and I guess with Blender, too.
the_Frog
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