As I mentioned earlier, Beryl summoned PHH Morgan who, upon finding that the British Lostbelt was only a barren wasteland with only the Tree of Emptiness present, hacked the Tree to modify the history of the Lostbelt. She only made one alteration to the Lostbelt: "Make it so Excalibur was never forged." Without Excalibur, Morgan believed, Artoria would have been unable to maintain her claim to the throne once Caliburn was broken, and Morgan could take her rightful place as King of Britain. Unfortunately for her, she thought as Artoria did, that Excalibur was forged specifically for Artoria as a replacement for Caliburn after Artoria broke it. We know better.
So! No Excalibur meant nothing to stop Sefar from laying waste to Earth. Only six fairies - the ones who were supposed to forge Excalibur but didn't - survived the cataclysm, and awoke to find themselves floating in an endless ocean covering the entire world, completely devoid of landmasses or any form of life. But there a few other survivors: a number of humans, led and protected by Cernunnos, the Horned God, last god of the world after Sefar had slaughtered all the others. He arose and approached the fairies intending to punish them for neglecting their duty, but he was too kind-hearted for his own good, and (speaking through his human priest) offered to make a new land for them to call home.
Naturally, they betrayed him, just as their descendants/successors would betray Lostbelt Morgan time and again. Poisoning his wine as they feasted to celebrate the deal, they used his body as the foundation for the southern half of their new land, with the corpse of the dragon Albion serving as the foundation for the northern half. But, of course, that wasn't enough to truly kill him, anymore than Marduk's axe-to-the-throat was enough to truly kill Tiamat. Cernunnos' existence was why Wodime (as a native Englander well-versed in British myth, he well knew what Cernunnos was capable of) ordered Beryl to destroy the Tree of Emptiness, as he was on par with the Foreign God and could have destroyed the planet itself.
As for Vortigern? When he materialized in the Lostbelt, he was severely weakened, and the little fairies in the Wales forest he arrived in mistook him for a prince, accidentally brainwashing him into believing himself to be Oberon. When Barghest (Fairy Knight Gawain) followed Morgan's orders to burn down the forest and kill him, she instead killed all the fairies who believed he was Oberon, causing the brainwashing to wear off after a while. By the time Chaldea has defeated Cernunnos, he's fully remembered his identity as Vortigern.
