You're missing the point. X1-The Wolverine still happened. We don't get to DOFP without X1-X3 happening.
X-Men-The wolverine happened to lead up the future of DOFP and wolverine
mission to past.His influence causes those films to be erased from contunity when he wakes up In new future.
If we ever follow up In new future then yes you would still have the mind of
the wolverine from Trilogy/The wolverine but it's question mark if you see that
wolverine again.The next wolverine solo film may be solo story In past post what
happens In Apocalypse.
Going forword into Apocalypse and other films these are only things that still
count in Contunity
Post credit scene of DOFP
The events of First Class
the 1973 parts of DOFp from wolverine waking up In bed to ending with Mystique disguied as stryker finds wolverine
the new future wolverine wakes up In
You could also count the WWII flashback of The Wolverine If you want to get
technical.
It remains to be seen If anything in future will come close to what went down
as we saw it in Trilogy.It appears the only thing they have to lineup with in future Is ending of DOFP.
From what was said in film the mind of wolverine In new future is all that remains of the non-FC films.The post-Apocalyptic future with sentinles Is gone as Is the "bad" X-men films Origins and Last stand but the "Good" X-Men films save for First Class and DOFP Itself are gone too.
When DOFP starts it Is 7th X-Men film but by end of film It becomes 2rd X-Men film.
The next Terminator film will start off as 5th film but by end of film it will be only film In Contunity.
The next Trek film untill title Is called trek 3 not trek 13.