Make the 2 meshes with their desire blend shape, then merge both meshes and now the 2 blendshapes should be in the shape key list, make both of them 1 of influence then create a new blend from mix.
Hope it can help you, im not 100 % sure its what your are looking for.
Alright figured it out myself, you need to tweak the goal damping value. Not too low and not too high.
Used a value of 1 for this one and it now looks exactly like the original. You can see that the original is also still there, since there's a small shading intersection where the green shines through on the right.
Yes there is a small reason behind this. This happens because when we remove a shape-key object's vertex data is changed to the current shape-key state which have to be rcalculated so for removing lags or software crash. That's why you can't delete shape key in edit mode. Whereas in concern to the materials the can be applied, removed and added in edit mode....
In edit mode, I selected the faces that I messed up (caused the problems) and searched for "Shape Propagate". This tells the Shape key to ignore the selected mesh. Then I was able to add new shape keys that didn't freaked out and worked just fine.
To keep your edits on the corrupted mesh, apply "Shape Propagate" first to your Shape key that changed this ...