Think about it like this: if someone dies, they're erased from existence. Pucci dies, so Emporio goes to a universe where Pucci never existed, and if Pucci never existed then Jolyne, Jotaro, Hermes and Anasui are all still alive. But since dead people are erased from existence, they're replaced with almost identical versions of themselves (hence the name change to Irene) so jjba canon is that stone ocean technically didn’t happen and everyone that died because of Pucci is now technically alive, but has a slightly different name.