Im not sure whats going on here but when I try to turn my polypaint into a texture map in zbrush the image below is the result. the image underneath is the polypaint ive done.
Just follow this tutorial. Automatically generated UVs are fine for the high poly sculpt. Just like baking normals, you can bake the diffuse texture from your high poly to better laid out UVs on your low poly.
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