The story you're probably talking about spans Young All-Stars Annual #1 and Infinity Inc Annual #2. It involves time-travel with the two teams facing Mekanique and Per Degaton.
Infinity Inc was a book originally set on Earth-2 Pre-Crisis in the 1980s and it continued Post-Crisis and it had to square its history with the new timeline somehow. Young All-Stars was a Post-Crisis book set in the 1940s that explored the new Post-Crisis version of that decade. To that end it replaced the 1940s Superman, Batman, Wonder Woman with Iron Munro, Flying Fox and Fury, etc.
The two-parter ends with the revision wave that replaces Earth-2 Superman in a classic JSA photo with the new history.
I think you're right that nothing similar was done with Earth-1 Batman or Superman. It was weird that after Man of Steel came out, the next month we had the Superman title rebooting old Superman lore from scratch like with Metallo, yet over in Action Comics he was meeting the Titans and they were recalling past adventures.
The piecemeal reboot was the cause of many problems and was part of why they did the JLA Year One series and the 1995 Year One Annuals to try to establish some of that Post-Crisis Earth-1 revised history.
EDIT: I mean if it's easier we could say that "Whatever Happened to the Man of Tomorrow" was the future of Earth-1 Superman and maybe The Dark Knight Returns is the future of Earth-1 Batman. Everything Post-Crisis is brand new characters.
It doesn't, and perhaps can't, make sense. The Crisis involved multiple Earths and in the new history, there was only ever one Earth. So there shouldn't have ever been a Crisis in the new history. Yet it's recalled for example in War of the Gods when Pariah shows up. Or in Zero Hour. Or in JLA Incarnations where they say the Crisis happened but the Anti-Monitor was attacking multiple time periods on the one Earth.
Wasn't the E1 superman though the one that morphed into the New earth superman?