Well, because Crono and co go back in time, and back into the future, history is changed.
We don't know exactly what happened the second time around. After Crono and co got teleported out, nobody knows.
That quote about "Melchior and Janus being warped into a gate" doesn't say when or where. It just says it happened.
The most likely probability is that it happened historically at the same time as it did in the original time line, so sometime later after Lavos awoke. All 3 Guru's could have been heading back there, and caught up to Janus, that was when he told Belthasar, or Belthasar knew himself from the black wind, even if he was on the continent or something.
The whole thing is very vague and problematic.
But then again, from Belthasar's perspective, it might also be that it's not that he knew Crono would die, but he simply calculated the chances that a hero would one day time travel, and try and go back to 12,000BC, and should one of them die, there is a back up plan, just like how Belthasar knew that time travellers would one day come and need his Wings of Time.