Did the Voyager episode Future's End occur in the prime timeline?

Question

The Voyager episode Future's End winds up sending the ship and its crew back to the year 1996. Is this 1996 part of the main timeline or was it a temporary alternate timeline created when Braxton crashed there in 1967?

I am curious because no mention of the Eugenics wars is made by the Voyager crew, nor do any of the people of the time bring it up. When Rain Robinson was questioning Tom and Tuvok the conversation focused more on them being Soviet spies, rather than maybe being part of one of the "supermen" factions that the world would have just been fighting. And Neelix and Kes, who were supposedly monitoring all of Earth's broadcasts, never seem to come across anything mentionable regarding it, but do think that soap operas are worth commenting on.

Answer 1

In universe answer:

You're spot on. When Braxton uses his "graviton distortion" to drag Voyager into the past, his own ship (the Aeon) ends up in 1967 which creates a new timeline. Voyager exits the same rift in 1996 inside the new timeline.

As well as the Eugenics Wars having not occurred, there are other anachronisms stemming from Henry Starling's exploitation of the technologies found inside the timeship, notably advanced micro-electronics, advanced scanning technology at the Observatory and his own use of subspace fields and holograms.

At the end of the episode, both the Timeship and Voyager are returned to their appropriate temporal and spatial positions. Aside from the crew of Voyager having knowledge of the incident (which never happened), the timeline from 1967 onwards is repaired.

BRAXTON [on viewscreen]: In my century we can scan time, much as you use sensors to scan space. The Temporal Integrity Commission detected your vessel over twentieth century Earth. I was sent to correct that anomaly. Prepare to follow me back into the rift. I'm returning you to your own time, to your previous coordinates in the Delta Quadrant.

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Out of universe answer

The lack of mention of the Eugenics war stemmed from a mixture of writing error and a genuine desire to retcon/ignore Spock's mention of the wars having taken place in the latter part of the 20th Century.

In an audio interview, Jeri Taylor spoke to this specific issue:

"I think that those of us who entered into the Nineties realize the Eugenics Wars simply aren’t happening and we chose not to falsify our present, which is a very weird thing to do to be true to it."

Brannon Braga identified much the same issues and (tangentially) referenced Future's End in an interview to promote 'First Contact';

When we did the Voyager two-parter when they went back to earth in 1997, Roddenberry had established that there were horrible Eugenics Wars in that time period. If we had paid attention to continuity and depicted the Eugenics Wars, the audience would have said, ‘What the hell are you doing? Are we in an alternate universe?’ The truth is, the people who know that reference from that particular episode of the original series is quite small in the grand scheme of things. There’s a great phrase on the Internet called ‘Continuity Porn,’ which means that there are continuity fetishists out there. People to whom if you just mention a name from the original series, it’s cause for celebration. It’s always a fun thing to do, and God knows we’re sprinkling plenty of that into this series, but we don’t let it interfere with good storytelling. The bottom line is that you have to take license.

Answer 2

In-universe, this is one of those instances where a closed time loop was interfered with and had to be corrected:

Chakotay: And every few years, there's been an equally revolutionary advancement in computers, all from Chronowerx Industries, all based on Starling's crude understanding of 29th century technology.

Janeway: Are you thinking what I'm thinking, Chakotay?

Chakotay: I wish I weren't.

Janeway: The computer age of the late 20th century-

Chakotay: Shouldn't have happened.

Janeway: But it did. And it's part of our history. All because of that timeship.

So no, there was no alternate timeline during the 90s. The anomaly mentioned at the end of Part II was simply Voyager's existence in the past, not the timeship in the 60s - restoring the timeship to the future would've set Earth back decades, maybe centuries, and not led to the timeline we know.

Within canon, an explanation for there not being any Eugenics Wars simply isn't given.

However, stepping outside of canon, authors recognized this problem and came up with a solution of sorts: The Eugenics Wars were a behind-the-scenes fight, more like a chess game with nations, and the general public did not know about the existence of the Augments.

This particular retcon makes it entirely possible that the Eugenics Wars did/are still happening...

To answer the comment on the question:

And don't forget that prime Braxton had no memory of it. This entire episode is kinda contentious, though Richard makes an excellent point that I'd never considered, in Braxton's own ship forking the timeline. I guess that basically solves it. – Lightness Races in Orbit

The original Braxton that went back in time was from further in the future than the Braxton at the end of the episode. That's why he didn't have memories of being in the past. The timeline split, if there was one, was either when Voyager left the 90s, or when Voyager returned in the 24th century:

Their existence in the past caused a younger version of Braxton to go and retrieve them, preventing the temporal explosion from happening in the first place - and splitting the timeline such that the explosion now occurs in a future that is not in the Voyager's future, but is still a possible future of the 1960s and 1990s - hence no paradox occurring.