I tried setting the flags manually in the PhysLevel.cpp which is where I thought it was stored.
PCookingParams.meshPreprocessParams = PxMeshPreprocessingFlags(0 | 0 | 0 | 1 | 0 | 1);
The first bit is supposed to be eWELD_VERTICES, the next is eREMOVE_UNREFERENCED_VERTICES, then eREMOVE_DUPLICATED_TRIANGLES, and also eDISABLE_CLEAN_MESH which is supposed to stop the welding of verts when clean mesh is off. Yet I still see that my verts are being welded. Which throws off the vertex index.