To me this is a very easy answer. After the events of the early 1970's happened,the mutants and the humans coexisted peacefully. Wolverine,up until mid 1970's happened but the events from the late 1970's at 3 mile Island never happened. Also X Men on(circa 2001) never happened.This means Everyone had no conflicts with each other. Wolverine was the only one who was completly lost when the space-time continuum finally remerged in 2001.This means Wolverine never lost his claws in Japan. 

X Men First Class was the official new beginning of the X Men timeline

I am sure i missed something but i think I am pretty close