My last post has the issue that you still need to sculpt the meshes after separation, which means that the edges along the seams that should always be connected are going to be difficult to deal with.
This might be a better alternative for your situation:
1. Start with your un-separated /un-rigged mesh.
2. create a copy of the mesh by selecting it and using the following script (or if you have Maya 2016 bonus tools you can use 'Duplicate as Mesh Reference' instead):
string $selectedShapes[] = `ls -sl -s -dag -lf`;
string $newMesh = `createNode "mesh"`;
connectAttr ($selectedShapes[0]+".outMesh") ($newMesh+".inMesh");
sets -e -forceElement initialShadingGroup $newMesh;
3. With the new (copied) mesh, split it up into the individual pieces (as you've always done), but keep ALL of the history as you do this.
4. Then with the original mesh, attach the blendshape deformer.
5. Now you can sculpt the blendshapes with the original mesh and because the separated meshes are connected with history, they will automatically update. So you no longer need to keep re-separating the meshes each time you make a change.
Note: I'm not suggesting you build this into the rig directly, but instead use this simply as a means of creating all the separated blendShapes quickly, which you can then export or make copies of (and so removing all the history).
So the general work-flow would be:
-add new target to the original mesh.
-sculpt it.
-duplicate or export (without any history) the separated meshes.
-go back to the original mesh and switch off the target, and create a new target... and so on.
Does this make sense?
Now admittedly, you would still need to connect the final separated shapes into the rig manually, but the whole splitting up process is more streamlined.
Hope this helps.
