Originally posted by cdtmDC's retcons, save for Crisis on Infinite Earths for the most part, are never taken seriously by posters. Case in point: all of Superman's post-Crisis encounters with villains named Zod. Geoff Johns' and Richard Donner's Last Son storyline basically retconned all of those away. Which makes sense since Infinite Crisis had just occurred and it was stated on-panel by Alexander Luthor as having altered history in subtle ways, thus allowing that to be the first encounter ever with a General Zod. That is... if you take retcons seriously.
If we did discard the fight because of the origin change, we'd pretty much have to discard the entire early 90's post crisis DC. Mon El, he had a major origin change too. To the point where a lot of his old stories simply doesn't fly with his new one. so does that mean Superman never fought an eclipsed Mon El and beat him? Does it mean all the events of L.E.G.I.O.N. never happened?
Out of convenience, most people don't. And no, there's no good reason why.