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Vertex IDs. If you add points, merge meshes, use external 3d editors or whatever, you will lose the vertex IDs that the game uses to identify points to morph.
The only known way to keep IDs so far is to avoid deleting or adding points in
milkshape, or use the
blender import and export, which can handle added points, sort of, by using the ID of an adjacent vertex.
Something, something, something, Darkside