A couple thoughts to avoid this happening in the future.
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Its best to create/rig a character at what you believe will be the final scale…of course your rig should be totally scaleable…but its just good to minimize the scaling as much as possible.
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Another thing to keep in mind is that you should finalize a model, delete all the history and then rig it. At the render stage you should plan on smoothing the mesh.
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When you apply a polySmooth to a bound mesh your painted weights will look like they do in your image. This is totally normal…the position of the verts added by the poly smooth are affected by the lower res smooth bound skin. You can’t paint their weights because you shouldn’t.
BUT in your case, since you mentioned you actually made some model tweaks…you have some options. You can use maya’s export skin weight maps to get image based weighting that you can then import onto your higher res mesh. I think you will need to export the weights from the skin before you applied the polySmooth and made the model changes…Of course you saved a separate version of your scene at this stage…I hope…It might work with the altered mesh…maybe.
After you have the weight maps exported just delete history on the mesh you want to use and bind it to the skeleton and import the weight maps you exported.
Both the “Export weight maps” and “Import weight maps” commands are found in the Skin > Edit Smooth Skin menu.
I say all this assuming that you have a usable UV layout for your character with nothing overlapping!!!
Because the weight maps are image based and not point based, it will apply weighting to all those new verts without much of a fuss.
Hope this helps.
~Ben