But in-universe, Star Trek: First Contact
wasn't a change in the timeline! They explicitly say so in VOY: "Relativity" ...
DUCANE: The Pogo Paradox.
SEVEN: A causality loop in which interference to prevent an event actually triggers the same event.
DUCANE: Excellent. Can you give me an example?
SEVEN: The Borg once travelled back in time to stop Zefram Cochrane from breaking the warp barrier. They succeeded, but that in turn led the Starship Enterprise to intervene. They assisted Cochrane with the flight the Borg was trying to prevent. Causal loop complete.
DUCANE: So, in a way, the Federation owes its existence to the Borg.
SEVEN: You're welcome.
In Trek's world, FC, ENT, TOS, TNG, DS9 and VOY are the prime universe. In 2233 an alternate reality branches off which is where the new movies take place. Any discontinuities are either mistakes or out-of-universe retcons.