There does not appear to be a clean solution for this. When you alter your mesh and the material order changes, it is expected that you re-assign the cloth to the correct slots.
If Skel Mesh Material Element order changes, Clothing assignments stay in the same order.
I don't know if there's a way for the editor to interpret the material assignments on import, but this can cause some problems when users/licensees reimport their meshes.
Result: ***Eyes_MatInst and JacketCloth.apx. Body Material is now Element 4 (this appears under the LOD section in 4.15)
Expected: Either all clothing elements are cleared or JacketCloth.apx is reassigned to Element 4
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-39995 in the post.