The reason your bodysuit invisible part became white is due to the naming convention of the suit with M4 body parts.  If skin appears as part of the suit's material group, synchronization will occur to every instance with that name.  As BB replied, you can specifically target your model by changing the "Apply Rule" in the VSSProp with the name of the model.  The procedures are clearly outlined in the manual. 

Again, you have 2 recommendation to offset future problems, either save the particular texture set as a texture group in the Material Room or save your character as a new figure after the changes.  I, myself, save the new figure, and if I modify the VSSProp, I save that as a new prop with a different name.  In my library, I created a special prop for Nybras because I added additional rules to target the character's material groups.