Zeref makes it clear that the world he's creating is entirely different for the current timeline, he says it in the second scan on the OP and
twice in this scan and makes a clear distinction between these different timelines.
Time Travel is treated weirdly in FT as unstable time travel makes multiple timelines such as when Future Rogue and Future Lucy came to the past, they made multiple branching timelines, where as when the Dragon Slayers came to the future the made the Space between time rather than a separate timeline.
The OP states that Zeref is reverting the entire timeline back 400 years, which would just be time travel on a universal scale which isn't what Zeref's doing. He's creating an entirely separate timeline that starts 400 years in the past relative to our current timeline that causes the destruction of the current timeline.