Hello!
I have encountered a situation where I need to export my model, which has texture and polypaint on it, and merge it to one subtool for exporting. However, when I cliced Merge under Subtool Master, my newly merged model didn’t have any colour. Instead he had big splotches of random colours, and his face was pale white (no texture was there anymore). I will upload a picture if requested. Please help! 
Try enable Uv Button in Merge before Merging down