I think eventually, even without the heroes' intervention, the Mystics and humans would have gotten along and shared various magics. Even if not, by that time Lavos was all hopped up on the planet's energy, so whoever had magic would have sensed some bad shit was about to go down and alerted folks of the doomsday coming up. Science would have investigated into the situation, found proof, and had domes built just in case.
They call it Lavos because that's what the Mystics called it, even in 1000 A.D. Our heroes just aren't into studying the old wars of 400 years ago or they'd know OF Lavos.