Yeah million/billion of Inchoroi with fully functioning scifi tech would have outmatched Earwa. Their reluctance to not blow up the world in pursuit of eden would have given the Nonmen a fighting chance with the first few battles, but I imagine that at some point they'd have either figured out how to safely graft magic usage, or made magic using weapon's races to kill the locals. If that didn't work, I think "fuck it, the trees will grow back, engage orbital bombardment" would have settled things. I mean, they planned to live there forever... Which is plenty of time to regrow some mountains post kinetic or laser based weapons bombardments.
Yeah, there is no "proof" but I think Ark,
alive, is the Progenitors or at least, heir to Progenitor-class knowledge. As such, Ark likely contained the sum-total generational, cultural knowledge that was off the charts comparatively. If it wasn't the Progenitors themselves, I imagine it was still an AI of massive power. Of course though, like anything else, that didn't make it incapable of failure. In fact, might have even made it more prone to it's own condition of death, in reality.
Still, I think fully functioning, it could have reverse engineered the Nonmen from scratch, devised manners and ways to undo them that were vast more subtle and effective than anything that later was scraped up from the bottom the barrel. Really, since the Inchoroi were just heavily indoctrinated, brain-washed, conditioned foot soldiers, it's really no wonder that asking them to reassess the entirety of the operation on their own, when they were made, from the get go, to be "ideally" conditioned for murder and not much more...