I guess The Avengers: Age of Ultron is going to be needing a few re-writes.
Nah. This is S.O.P for Marvel. They make a “big” change in the comic books in between movies and then return to the status quo in time for the film. See, e.g., the “death” of Captain America, Dr. Octopus as the new Spider-man, Mr. Fantastic as a villain, etc.