I heard that Amalgam-related events were supposedly canon for both Marvel and DC (though for obvious reasons they could never mention them in their personal comics). And there is JLA-Avengers, which is also supposedly canon for both of them, but the two things aren't canon to each other. I understand the real reason is most likely that Kurt Busiek didn't want to deal with this stuff, but I wonder, if there exists an in-universe explanation?
The second mini-series follow-up, Unlimited Access might hold some clues here, as it implies that the heroes from both worlds tend to forget about the other world after some time (as such, Wonder Woman doesn't know who Access is, despite having met him in the previous mini-series, All-Access). In JLA/Avengers, the heroes find a way to cross the universes that don't involve the two Brothers, but as they don't remember their previous team-ups and amalgamation, it would have been like the first time for them.