I just answered this question myself. By choosing unset instead of set for the sub-assembly, it seems to revert to the last saved colors for the subassembly. At least it worked in this case.
Thanks anyway.
I have a assembly in Pro/E 2001 made of several sub-assemblies. If I change the color of the sub-assemblies parts (In the sub-assembly model), they don't change on the top assembly, even after re-generating. Do I have to re-assemble the top assembly with the sub-assemblies new colors? Aren't...