My personal (not very well thought out) theory is that changes only ripple forward in time, not back (in this particular instance — not in all Trek instances and certainly not in all sci-fi time travel instances, in all honesty, time travel works the way the narrative needs it to work).
So, since the Diviner travelled back to the past in pursuit of the Protostar (whether with or without Chakotay and Adreek on board), as long as none of the parts needed (the “big dominos”) were missing at the time they came into play, everything that happened prior to Season 2 happened as we saw it happen. So Gwyn was still created and there was still an enslaved populace mining in an attempt to locate the Protostar, etc.
It's actually well thought out. Changes go forward, not back.
Gwyn was created, before season 1 and "again" during season 2 (when the Diviner was explicitly shown to go back in time from the destroyed, future Solum - once again), by the Diviner travelling backwards in time through the timey-wimey wormhole. Both times, the Divinir created Tars Lamora and Gwyn and thus changed his past. The second time, they had to make sure the Protostar would end up at Tars Lamora before the Diviner arrived though, otherwise he would have no reason to go there (I suppose he followed its warp trail or something like that, having had the luck of exiting the wormhole close in space and time to the Protostar's own exit).
Note that the Diviner created an alternative timeline with his actions. In the original one, which we could call the "prime timeline" were it not that the Prodigy characters aren't actually following it, Solum was totally wrecked by civil war and no Gwyn exists. In the changed timeline, he created Tars Lamora and everything on it, creating a branch timeline where he had a shot at preventing Solum's destruction. He eventually succeeded in that, through his "progeny" and also partly due to other changes he made (like getting the Protogies together and in close contact with admiral Janeway), though not in the way he had planned originally (by using the weapon onboard the Protostar).
When the Protogies "fixed" the timeline in the end, it was the timeline that the Diviner had created before and during S1 that got fixed, by putting its missing piece (the Protostar deeply embedded in Tars Lamora) back in place. Nobody, not even (old) Ascencia, wants to go back to the original timeline that had Solum getting destroyed, Gwyn not existing and the other Protogies likely never meeting each other.