There was a tiny bit towards the end of Watching the Clock
, where some doubt is cast on whether the 29th and 31st century time cops represent the same future. Amusingly, it seems as if they themselves weren't entirely sure.
And you only have to look at "Shockwave", "Twilight" "Azati Prime", "All Good Things", "The Visitor", "Future's End", "Storm Front" etc. to see how easily the future of Trek shifts and changes. How many Trek stories about the distant future take place between blasts of Annorax's weapon, where entire species that play a pivotal role in one timeline are deleted from existence?