It's not like they are doing this randomly though. They said they've been planning the plotline for 15+ years.
Whispers were fate who tried to keep the original events in place. The new plot so to speak of FF7 remake is that the original happened along with Advent Children, Sephiroth didn't like how that ended since he "died", and as such he goes back in time? and tries to change fate, and manipulates the party into destroying it. The end of remake is a new timeline, still the same as the last, but now without "fate", it's open to change. As far as I know, everyone is unaware of this so far, even Aerith. Though in the short stories (canon) spanning the time between the original and Advent Children, she did learn in the lifestream that Sephiroth is tied directly to Cloud. As long as Cloud even remembers/knows of Sephiroth, Sephiroth can be reborn.
But if Crisis Core doesn't change in the remaster, then the game still features the first timeline before something changes when they destroy fate. However, that change in the end of Crisis Core would be timeline 3, since when they do exit Midgar in the FF7 remake, Zack is still dead.
It's very Nomura.