The original Crisis on Infinite Earth’s was much a comic book story as it was a marketing and restructuring of DC Comic’s publishing line. Since the early 1960’s DC had operated under the concept of a Multiverse: an infinite number of Earth’s. This too was motivated by the business end of the comic book world. By 1985, DC’s continuity was an unruly mess and far too complicated to understand, and so the decision was made to collapse the Multiverse into a single, shared continuity similar to that of Marvel’s fictional universe.
However, owing to the Multiverse, there were versions duplicate versions of Superman and Lois Lane, and unfortunately for the Golden Age versions their Earth would not survive. Nor would the Earth’s X and Prime, belonging to Alexander Luther Jr. and Superboy. An editorial edict from DC that post-Crisis there was to be only one surviving Kryptonian and that was Earth-1’s version of Superman. To underscore the point, John Byrne was brought on to reboot Superman’s continuity to reflect the editorial edict.
With no room left for a Supergirl from Krypton, and the Golden Age Superman that as a young Superboy traveled to the 23rd century to hang out with the Legion of Super-Heroes; much less the original Superman and Lois Lane. So, without killing off the Golden Age icons, Alexander Luthor Jr. constructs a pocket “paradise” dimension for himself, Superman, Lois, and Superboy to live on outside the reality of DC’s post-Crisis universe.
Gone, but not dead is the best way of phrasing their status in the twenty years that followed. They never again appeared in mainstream DCU continuity until 2005’s Infinite Crisis #1. By the end of Infinite Crisis both characters meet their end as the Multiverse, albeit a limited version of it with fifty-two Earths, is reintroduced.