It’s never been in any way realistic that most of the time travel incursions didn’t somewhat change the Prime continuity.
There are exceptions with the Guardian of Forever’s intervention, but First Contact and Voyager’s temporal interventions had to had changed the small things.
Besides, Roddenberry himself decided to change the timing of WW3 and the first human warp technology in TNG Encounter at Farpoint. There has been a change in continuity since at least that point.
This actually makes sense of it in-universe and in terms of physics.