This situation relies on Reddit user /u/PepperBeef2Spicy's interpretation on the ending of Stone Ocean.
In short, Pucci did create a new universe. However, it hadn't completely caught up and erased the old universe. The new Made in Heaven universe completely collapsed, removing Father Pucci from existence and Emporio back into the original universe. Since DIO and all of his associates were destroyed in 1987, Pucci never framed Jolyne, Annasui, Weather Report, or Hermes, and they were never in prison. Jotaro also never had to take care of the fallout from Enya or Pucci, and was able to become a good man, and take care of Jolyne.
Irene, Annakiss and the new Hermes and Weather aren't new souls, but rather the best versions of themselves they can be, now that they live in another place.
