I'm sorry? That's not a change. The fight against Darkseid isn't considered the first meeting of the Justice League, just the first time
several members fought together.
The next page explictly states the Justice League wasn't officially joined until the
Appellaxian invasion. This is from JLA Year One in Post Crisis, and that series explictly states many of the pre-Crisis adventures still happened. That's not removing anything, that's saying "this one happened, then this one happened"
Again, this isn't "Oh the universe had a massive change" this is "we put these post Crisis events back into the universe" which is what the comic literally said. That they were putting things back into play.
They even explictly state IN UNIVERSE the last reboot was the n52 and it was undone.
To use the same logic,
Post Zero Hour a lot of things changed in universe without it being a full reboot: Batman never caught his parents' killer nor does he know who the murderer was. Batman was never a member of the Justice League. Finally, Talia (daughter of Ras al Ghul) never had Bruce's baby. Bruce Wayne legally adopted Dick Grayson. During his days as Robin, Dick Grayson had a traumatic failure during a confrontation with Two-Face. Catwoman's origin was also largely revamped
Same for Infinite Crisis which also effected a ton, including Superman getting a new origin, The alterations of Jason Todd's origin after
Crisis on Infinite Earths and his resurrection, the Doom Patrol getting their origins rebooted and then unrebooted, Joe Chill being arrested for the murder of Thomas Wayne and Martha Wayne, Superman's "Legion" membership being re-retconned in, Power Girl getting her Pre-Crisis history back, Earth-2 Justice Society being a thing again. Etc.
In all of those, we don't treat them as entirely separate versions, just the same Post Crisis universe since narratively, it's supposed to be the same Post Crisis universe but with alterations.
And here, narratively, it's supposed to be the same Rebirth universe but with alterations.