I think you have the right workflow (edit in Premiere, replace with AE composition). You could duplicate all the clips where VFX and place them on their own track. Then highlight them all and replace with AE composition. That way you have non-destructive replacements.
I take it reshooting isn’t an option?
Left-field alternative – what about using Character Animator, drop the actress’ footage into that and replacing them with a cartoon talking head?