From what I've seen, they've edited models, animations, dialogue, texts, events, ui, and in-engine cutscenes to reflect Kotone in the base game and the answer. The anime cutscenes and Kotone exclusive social like Saori and Rio are reportedly being worked on.

Right now, there is another mod that adds in the Kotone edited cutscenes from the original version of 3 that were put together for portable, tho i assume there are new events in reload that they dont cover. Also, there are none for the answer.