User blog comment:HollowIchigo58/High School DxD Season 4 Announced/@comment-4547267-20161023044210/@comment-9595671-20161024075141

It likely still connects from the BorN timeline though, if only because redoing Season 3 would confuse the fans who only follow the anime. Though they'll probably avoid directly mentioning the previous season's changed events so it still goes the way it normally did.

I guess another way to say it would be after how Season 3 ended, the changes that Loki caused by going back in EX have stopped from here. So in a way aside from a few minor differences (like Issei not escaping the JD from the Oppai Dragon song) the timelines are reconnected in a sense for Season 4.