It's worth pointing out that the 1996 seen in "Future's End" was probably an alternate timeline anyway, since once Voyager restored the timeline, Braxton had never gone back in time at all and thus the 20th-century timeline resulting from Starling getting his timeship was undone, presumably replaced with the original version of history.
I remember John Ordover and I once spent an hour or so on the phone trying to figure out whether the events of "Future's End" had been erased from the timeline or not. In the end, we never did pin it down, which is why I largely ignored "Future's End" in my Eugenics Wars books . . ..