In the original timeline, the end of The Wolverine is where Logan finds out that Charles Xavier is still alive after the events of The Last Stand. But since The Last Stand didn't happen, neither did that.
As a matter of fact, since The Wolverine came out prior to Days of Future Past, there's no knowing how many of the events of this film were left intact after the X-Men's temporal meddling, and they could very well have all been wiped out of existence. Since Logan's trip to Japan is never mentioned again, it seems a pretty safe bet that most or all of The Wolverine never took place.