Pretty sure the Mageddon event was either non-canon, happening in an alternate universe, or followed immediately by mass amnesia. Because nothing else in the DCU subsequent acknowledges it, and a vast number of things in the DCU subsequent contradict it, and at that point the problem is no longer with the subsequent stories, but with the Mageddon event itself.
Not the last time Morrison tossed out a Big Neat Idea without any concern for the ramifications it would have on a shared universe, but at least back then he didn't have the clout to keep everyone else from cheerfully ignoring him and continuing on with their own stories as appropriate.