''After Wade and Logan saved the FoX-Men universe from the Time Ripper, the universe regenerated with Unheroic Logan becoming the FoX-Men Wolverine. The FoX-Men Wolverine was erased, but the events of the past remained the same, only now, the universe "remembers" Unheroic Logan as the one who lived them. The aura of Earth-10005's Wolverine lives on in him, making it feel like he was always the Wolverine of that world. The past is intact, but the future is brand new.''
Also, I have this headcanon: ''Wolverine and older X-23/Laura prevent Xavier's dementia and seizure by giving him early treatment, Beast will create an medicine to Charles, starting in 2024, after the events of DP&W, to not causing the Xavier's incident, since Laura knows about the Weischester's incident of 2028, mentioned in Logan. Also they go after Essex/Transigen organization very early, with X-Men, before 2029, they will also save the young Laura and X-23 children early too. The events of Logan will not happen after the events of Deadpool & Wolverine.''
I will use this headcanon, because will be weird when the X-Men appears in Doomsday with DP&W's Logan, without/instead FoX-Men Wolverine, so if didn't have a explanation, I will use this headcanon.