If you just duplicate some faces out of a mesh and assign the new meshes to the original as targets, the vertex numbers would not be the same. No good!
What you need to do is to make sure you have a blendshape node on the mesh, preferably assigned before you assign the skinning. Alternatively you can assign it after the skinning and move it down so it evaluates before the skinnode (deformer order), but in a few situations Maya woun’t let you do that, and then you might be stuck…
Add a blendShape node to the mesh (you don’t need to give it any targets)
Make a copy of the mesh , that you can later duplicate to make your targets. Call this. e.g. BaseShape and hide it for later use.
Then rig, add skinnig, animate and do whatever you like on the original mesh. (Exept messing with the meshes components, other than with deformers)
At any time you now have the blendshape node in the right place (deformer order) and the BaseShape copy that you can use to make targets from.