Quote Originally Posted by The Dying Detective View Post
X-Men and Avengers have done their fair share of weird things to their continuity too. Like the infamous return of the founding X-Men's younger selves which should have brought issues to the timeline and thanks to their exposure to the current era no one really knows how they will affect time in the present if they were to return to the past. Of course they could have wiped their memories clean and fix the problem but that's doesn't seem to be an option for some reason. Instead for a couple of extra bucks we're getting this big crossover even that may or may not alter things. And let's not forget what happened to Captain America becoming a Nazi and instead of reverting things back to the way they were we now have a alternate version of Steve Rogers who was good running around instead. And I believe some sort of weirdness was done to Iron Man but I forget what exactly it was and hwo they even rectified it.
All of what you're talking about has been explained in Marvel continuity.

The O5 X-Men will eventually return to their time and its been explained that they weren't missed because some new version of the Brotherhood went back in time and masqueraded as them in their absence. Also, the version of Steve Rogers we have now is just the regular version having returned. The Nazi Steve Rogers was the one who was turned into an alternate version.