Actually, I think you CAN fix this. If you set a vertex group to the shape you messed up then the shape only affects the parts within that vertex group correct? So the rest of the model is back alright. If you add a new shapekey with that messed up shapekey WITH a vertex group assigned, it will create a new shapekey exactly like the previous one, only without the vertex group. The vertex group information is kinda “baked” into the newly created shapekey, so you can start fresh and still keep the parts that are right.
Organising your shapekeys is another thing though… it’s hell.
Like Bugman said, you shouldn’t be removing vertices as in DELETING them from the model, but that is NOT what you are after right? you only want their appearance in the messed up shapekey to be “reset” right?
Easy to fix. add a vertrgoup, and duplicate the shapekey, it will be a fresh one without the vertgroup, and without the mess ups.