Thanks for your reply, CAgameDEV.
Are you adding geometry, removing geometry, or altering the UVs? You'll run into issues if so...
Yes, and I want to know exactly why. Because in some situations Polygon Fill is superior to ID masking.
If I would know exactly what happens behind the scenes, I could maybe counteract when editing the mesh.
For example if the masking is based on the vertex ids, then mesh edit operations, which do not change the vertex order, would be valid.
Otherwise make a color id map and use that to mask for your fill layers.
Yes, that is also our workflow currently. But it is not perfect in all situations.