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This question already has an answer here:

At the end of X-Men: Days of Future Past, we see Wolverine

wake up in a new timeline.

After a few “surprises”,

he sees Professor X, and Professor X senses that this Wolverine is not the Wolverine from his timeline.

What happened to the Wolverine in this timeline?

marked as duplicate by Valorum, The Fallen, Jason Baker, Ward, user1027 Nov 27 '14 at 15:36

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Presumably he got overwritten by the Wolverine from the other timeline, just like everyone else who went to the past and came back. For most of them it was just minutes, not enough to make them a different person, but in his case it was decades.

It is disturbing but similar things have happened in other films.

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