However, this all goes horribly wrong by "Who Saves the Saviors" and "Temporal Mechanics 101." Instead of Chakotay sending the Protostar on autopilot — as everyone assumed he did in the original timeline — he goes with the ship, which means it ends up stranded in 2374.

This basic event is the crux of the near entirety of Season 2. In order for the timeline to be restored, the Protostar has to get back to Tars Lamora, which is why the kids have to team-up with Chakotay to get the Protostar back to where they belong.

None of them would know each other, Gwyn wouldn’t exist, and the Federation wouldn't be saved from the Construct if they didn't. In addition to a lot of other adventures, the big arc in Season 2 is designed to preserve the backstory of Season 1.

And this is the issue that I have with the outcome of the story. After all they did to "restore the timeline," we still have a past in which Gwyn shouldn't exist, because her father never goes back in time to enslave Tars Lamora and become the Diviner.

While I'm sure there's a way to logic it away, it seems to undercut the entire season, and what they were trying to accomplish.