And it was now I realized 'The House With a Clock in its Walls' made a JoJo reference about resetting the world.
Anyway it may have brought every death in JoJo back to life. So that means Dio wouldn't have Jonathan's body, but considering his body may have limited Dio's vampiric abilities (unless he actually was being such a dick), Jotaro would've actually had a hard time dealing with Dio.
Dio would've still procreated Giorno but Giorno would've been born with a villainous mindset and could've, out of any, inherited The World, overthrown Diavolo, or team up with him. Giorno could have also inherited vampirism from his father.
Jotaro might've not actually made it into part 4, but Dio may have instead, though I don't see what kind of antagonistic role he would play.
Oh wait, he could've already been eaten by the Pillar Men going on in his vampire life.
So what now?