You are hung up on the difference between transitive and intransitive verbs.
An intransitive verb does not take a direct object. For example, a cat can catch a mouse, and a cat can eat a mouse, but a cat cannot "die" a mouse. Catch and eat are transitive; die is intransitive.
Many verbs can be used transitively or intransitive. The cat can eat a mouse, or she can just eat, and the contents of the meal are just assumed.
You can say, "The emphasis shifts". It's common enough to say something shift, even if something inanimate being acted upon by an external force.
Or you can say, "The change shifts the emphasis." Either way.
In your sentence, there is an argument to be made either way. "The emphasis had been shifted" is a passive, transitive use; while "The emphasis had shifted" if the active intransitive. In general, I prefer active, but here the subject of conversation is really the changes.
You might cut the Gordian knot by writing "The modification they made in the draft was so drastic that it shifted the entire emphasis."
(Note that I made "modification" singular so I could use "it" and that I got rid of the passive "made by them".)