I forgot about Magus saying that(on the Cape)...
on Lavos being summoned in 600 AD and Magus in the original timeline...
Belthasar: Lavos disappeared briefly when he was summoned away by a mighty wizard who lived in Guardia, in the year 600.
Lavos was successfully summoned by Magus in the original timeline, because Belthasar pretty much knows everything. The word 'disappeared' does not leave room for the possibility of a partially summoned Lavos.
something else I noticed...
In Enhasa, Janus tells the party that the black wind is blowing, and one of them will die soon.(couldn't find the exact quote)
Then in Zeal before Crono & Co get captured:
Janus: The black wind...
Schala: You feel it too?
Both Janus and Schala can sense this black wind, which seems to mean that someone's gonna die. Crono dies, so Janus's prediction about the party came true. Also, it can be said that Zeal dies(the place, not the queen).
When you go to fight Magus in his castle...
Magus: Ah... The Masamune!!! I bet you're just dying to use it! The black wind begins to blow... Okay... give me your best shot... If you're prepared for the void!
Since Magus is a no-nonsense-let's-get-this-over-with kinda guy, I doubt he was mentioning the black wind in an effort to be ominous, I think he really did feel the black wind. Now, here's where it gets interesting...
At the Ocean Palace, when the Prophet reveals himself to be Magus...
Magus: I’ve been waiting for you, Lavos. I swore long ago... that I'd destroy you! No matter what the price! It is time to fulfill that vow. Feel my wrath, Lavos!!
Magus attacks Lavos...
Magus: Wh, what...? It doesn't work?! Aughhh!!
Magus was shocked to discover that he could not hurt Lavos. After Crono dies...
Magus: I can't... beat him. Lavos...!
Magus summoned Lavos with the full intention of defeating Lavos, not knowing that he could not take Lavos on by himself. From what Belthasar said, we know that Magus successfully summoned Lavos in the original timeline, and Magus had no idea that he could not hurt Lavos. Magus felt the black wind in the changed timeline, and the black wind has a pretty good track record. Since the interference of Crono & Co at the castle were not part of the original timeline, and since Magus cannot hurt Lavos at that point, the black wind Magus felt must have been for himself. Therefore, after successfully summoning Lavos, Magus was killed by Lavos in the original timeline.