If you're as old as I am, you remember the hype that surrounded the Death of Superman even before the first issue hit. Doomsday's origin was speculated on by many, along with how Superman would return from the dead, if at all. Speculation abounded that DC had quietly introduced the means for Superman's return via the Walt Simonson Superman Special, which updated the Sand Superman storyline by Dennis O'Neil and cemented it as part of the post-COIE canon. At the climax of the issue, the art and dialogue is vague as to which Superman survived the battle: the original, or the sand duplicate, which had now fully become Superman.
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DC didn't acknowledge the story in the main Super titles, but speculation has arisen over the last few years that the Superman who died fighting Doomsday only to later return to life was the Sand Superman. Fans of this theory suggest this is why Superman's powers were out of wack for a long time following his return, including an arc that saw his powers make him too dangerous to remain on Earth. That arc eventually resolved, but Superman lost his powers during Final Night, which eventually fed into Superman Blue.
This article makes a number of interesting points in its suggestion that the real Superman died in 1988 and was replaced by a doppelganger that was, for all intents and purposes, really Superman. The fact that he wasn't, however, means that there were various power issues and that kryptonite played a role in restoring him to full power in Superman #82.
Let's consider for a second that the real Superman survived the battle with the Sand Creature. We never see what happens to it after it fully becomes Superman and is knocked unconscious or killed. Did Superman keep the body in the Fortress? Did the body return to a sand-state?
The story was never referred to again, and the only reference to the Sand Superman saga (pre or post-COIE) came during the Action Comics Future's end tie-in. The issue was written by Sholly Fisch, but the series itself was overseen by Dan Jurgens. The Sand Superman in this possible future imparts a measure of Superman's powers to regular people because the real Superman has given up his superhero career.
Whether or not the Future's End issue has any bearing, could it be that Manhattan, needing a Superman for his New 52 revision of the DCU, used the replica Superman in the Fortress? This would explain New 52 Superman's appearance after his death. This would also mean that New 52 Superman is still a duplicate of Superman, a la Superman Red, but has not only lived his New 52 life, but also shares a good portion of the post-COIE, pre-Flashpoint Superman's as well.
Let's go another way with this theory: what if the real Superman did die? The climax of the Special certainly makes it seem as if that's what happened. If Zero Hour and the other temporal crises that followed didn't erase the story, have we been dealing with a fake Superman all this time? If so, the Superman that became the New 52 Superman would be the real guy, assuming any of this plays into Rebirth and Superman Reborn.