The cut scene after Hokkaido made it kind of obvious that Providence was somehow involved in the cloning project. It would make sense that Ort-Meyer was looking for other ways to fund his work after the other fathers got impatient and cut their funds.
Obviously they retconned some stuff like the clones already carrying out assassinations or 47 and 6 being friends, but these are only minor retcons that don’t change much. I even like the idea of 47 already being a killer. As long as they don’t retcon the Five Fathers, the story of the first game still happened. Of course, the last page of the comic shows the Asylum in flames but I’m hoping that this is just the imagination of 47 and 6.
While I don’t have any complains about 47’s part of the story I really don’t like Diana’s. It just doesn’t fit her character at all. And making 47 one of the murderers feels like a bad idea that was only done because the story needs some dramatic reveal in the near future. I really hope they never bring that up in the game.