Thank you for your reply. I've to remove inside footwear in order to combine "footwear + feet" as one mesh (Left + right separately). The rest of UV map stays intact as it is. Would I be able to replace UV map still into substance and that means adjust footwear on painter slightly?
UPDATE: Look like I may need to import the whole UV map and baked the mesh again. As a trade-off, now I am looking to save the LAYERS with smart materials and skin. Then quickly paint the model using polygon fill.
Now my question is to save the layers with smart materials. Can I do that?