Use quite easy and stupid approach like it used for shape keys: re-make editmesh (editcurve or editlattice) before creating index array for hook or storing vertex index in parenting object. Even if hook was added in "current" edit mode, it should be re-mapped on loading edit data because topology could be changed after it was created. Such kind of re-loading edit structures is the easiest way for now to update keyindexes to relevant state. Also, fixed bug with not re-mapping indices for vertex-parented objects. Really old error, not sure why it wasn't noticed yet.