^The 29th century time cops in "Relativity" called First Contact a "pogo paradox", where interference to prevent an event is what causes that event to happen.
Therefore, there was only the one version of Cochrane's flight and Enterprise was "always" the past of TOS and TNG. It's a (big) out-of-universe retcon, not an in-universe altered timeline.
But remember the ENT-E crew saw the 24th Century Borg Earth while they were in the temporal wake following the Borg Sphere. That means in one timeline the Borg succeeded in assimilating Earth. The ENT-E prevented this timeline by destroying the Borg and restoring enough of their recorded history to what it should resemble. No doubt their presence made this timeline of 2063 different moving forward. With VOY 'Relativity' 7 of 9 has recollection of both timeline of events. The future where the Borg succeeded in assimilating Earth and the future where the ENT-E prevented the assimilation. It's impossible for her to know about both of these, and it can't be a paradox if it was destined that the Borg would both succeed and fail in the same time travel endeavor. Chock that up to another Voyager writing staff goof. Just press the reset button and it'll all seem alright.