Hi! I've attached a file where you run a script that copies the vertex coordinates from a second mesh into the Basis shape key of the object.
The copy operation works well, the thing is that the the existing shapekeys don't take into account the changes of the Basis shape.
You may find that perhaps I'm missing something in the script, but I'm reporting this cause I've seen this same behavior in my everyday modelling workflow, only that I could never recreate the bug. Sometimes when going in and out Edit mode or Sculpt mode, I realize that the existing shapekeys have gone out of sync with the changes I was doing to the Basis shape... It's like if the changes of the Basis shape didn't propagate to the rest of the shapes.
So please, give a little check to the shape keys code, perhaps you'll find out why this could happen.