We don't know how wolverine is time traveling, if its mind switching the question is how is he doing it? its possible if wolverines body is still in the future unconcious in some way while his minds in the past and as he changes the past we see the future change around him each time, its possible maybe he says something to Xavier which changes the future with jean and scott resulting in them being alive at some point in the film fighting sentinels but the dark future is still the same for that time being till the end when they stop whatever it was that starts this dark future
well thats if the film does cut back and forth like wolverine and the X-men did
after all singer did say
“We also wanted to play with the notion of different times and stuff like the way that time affects destinies."
It's reasonable to think we could see time change around wolverine in the same way time effects destinies every so often when something different happens in the past we see how it effected the future, but obviously wolverine isn't effected
Hope I explained that ok, is a tough thing to explain