Are you deleting history or something? Make sure if you need to delete history, use "delete non-deformer history" otherwise you will be deleting your skinCluster nodes too.
History means ALL history. Deformers included, That way you can build your mesh one way, apply a lattice or other deformation to it, alter the mesh then remove the deformer but keep the new vertex positions. non deformer history is just the other history bits like your polygonal building operations.