Board Thread:General Discussion/@comment-8284722-20130524162626/@comment-61022-20130811180330

Likely the explanation is much like the Age of Apocalypse and House of M. Character tries to change history on Earth-616 actually creates an alternate reality that overlays the Earth-616 until the time paradox, reality shift, whatever is reversed then Earth-616 is restored to the status quo while the alternate timeline endures independently.

Characters who are aware of both histories and timelines (such as Wolverine in the House of M) Could be considered a merge of the House of M and Earth-616 Wolverine from the point of awareness, as once the House of M was removed from the Earth-616 universe it continued on independently with its own Wolverine and Earth-616 Wolverine returned to his native reality.