The problem is Star Trek is never clear on which method of time travel it uses. It goes between both the one timeline Back to the Future thing and the quantum universe thing (every possibility does happen, creating a parallel universe and an alternate timeline/reality like the Worf episode) whenever it suits the plot. The most famous parallel universes in Star Trek are also usually shown as evil universes that have existed for who knows how long where everybody has evil goatees and not explicitily the result of time travel creating new branches.
Most of Star Trek has been the single timeline thing, or when they have messed up the timeline and created an alternate future/past, they fix it and get back to the same one they came from again. There's even a police force that fixes the single timeline whenever somebody messes it up in the future in Voyager.
When Kirk goes back in the Guardian of Forever, they accidentally create an alternate reality where the Nazi's took over America and Starfleet doesn't exist and the Enterprise disappears, etc. but they fix it and then get back to exactly where they started. When they go back time in ST IV, they get the whales and end up back at the same future they left (otherwise, there are near infinite number of universes out there where Kirk didn't come back to that universe and earth was destroyed for having no whales). In Yesterday's Enterprise, the same thing happens as in movie (ship comes through a temporal distortion - when arriving it creates an alternate reality where the Federation is at war with the Klingons for 20 years...but they send Enterprise C back and everything if fixed again. But in that case, they sent it back through the same way it came and it was said to have arrived back where it started as if it had never left.
Maybe in Star Trek XI, because the Naranda hung around for 25 years and never went back the same way it came, things were irrevocably changed.
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