Polygonal mesh CV's (control vertices) doesn't exist, that term is either applied to NURBS surfaces or curves. Did you mean UV's or your talking about NURBS surfaces?
If you are talking about polygonal meshes, the ordering of you face id's are dependent on Maya mostly. If you edit your mesh maya reorders the vert/face ID's to it's liking. Mainly for performance purposes. You would either have to reconstruct the mesh face by face via the API, what is tedious task to have in a controlled manner (check the "meshReorder " plugin example in the maya api documentation). Or use some kind of other method like, vertex color / metadata to tag your geo.
J