what I usually do - pose the skeleton. duplicate the geometry - tweak it - delete history + blindnodes - connect as blendshape.
which means you can disconnect/connect your blendshapes as often as you need. it does not make any difference as long as you don´t delete history on your bound geometry. but blendshapes don´t get enveloped to the skeleton, so -
explain to me if I got something wrong?
everything starts and ends in the right place at the right time.