If Lavos can travel through time then couldn't lavos have destroyed the entire world during the zeal incident because the lavos we see in 1999 would be the same as the lavos from zeal?
Maybe I'm thinking too hard or something.
The question isn't 'could he have destroyed the world earlier' but rather 'WHY he didn't destroy the world earlier. I personally follow the view that Lavos only rose to combat percieved threats to itself. During the time of Zeal when they were draining his energy, he rose and ended their society (but left the world itself intact, so he could continue to harvest DNA). During 1999AD human society had reached the point that it could pose a threat if they discovered his existence, so he caused a worldwide catastrophe.
Lavos came to our world to harvest DNA and it would seem counter intuitive for him to destroy the planet and end his harvesting early without some sort of threat. That is why he doesn't simply destroy the world earlier, and why he DID rise in 1999.