If I remember correctly, Nasu stated that Zeus merging with the other Machine Gods "merely" gave him the power to go even with Sefar and repel her, implying she still was destroyed by Excalibur in this timeline (she doesn't seem to be around by the time of the Lostbelt and I don't see the Velber going "Welp, we give up" considering their habits or Sefar herself deciding to simply go away, plus the Gigantomachia still happened and Giants in the Nasuverse are the reamnants of Sefar so she was probably destroyed in that timeline and since the only thing at that time that could fight and destroy her was Excalibur, this implies the sword was still forged). Apparently (I say that because I don't play the game so I'm not sure if he has this in-game) this is supposed to be represented by Zeus's skills in the game, each one representing the wars he has won, the Titanomachia for the war against the Titans, the Gigantomachia for the war against the Giants and the Olympiamachia for the war between the Machine Gods, yet he lacks a skill for the Leukosmachia (the war against Sefar, with "leukos" meaning white) which should be there if he really did win by himself.
MC: Can you explain a bit more about how the Atlantis Civilization ended?
Nasu: Well that is the Type Moon World story right? In the Type Moon World, 14000 Years ago, Sefar came in and went around breaking down everything. Gods from other sect of divinity when Sefar arrived reacted it "Oh no a threat beyond the sky came down, what do we do?" and panic-ed and started making plans. While Atlantis because they were from space too, they were looking down at them a bit (laugh). They were acting very high and mighty, until they were easily defeated because of Sefar being an Anti-Foreign Civilization Specialty Weapon. Meanwhile, in the Greece Lostbelt, Zeus alone recognized "This is Dangerous" and immediately recognized, and forced the other 12 gods who didn't wanted to fuse, and forced them all with "If we don't fuse now, what do you think is gonna happen",and fought Sefar to a draw and chased it away. But in a normal Type Moon Senki World, the 12 Machine Gods didn't become serious and as a result Atlantis Civilization ended. And surviving remnant flowed to the Aegean Sea, which later became the foundation of the Greek Civilization, type of almost forceful story happened.
I have a link for the proper interview but it's in Japanese and I can't read a word of it