This is something that bothers me a little about recent Doctor Who. A big part of a recent story arc revolved around rebooting the Universe (literally), so certain alien invasions never happened, and the Doctor is less known throughout the universe, including to his age old foes, the Daleks.
It was all really faffy and unnecessary. In a show where time changing happens all the time, you should just play it by ear on an episode by episode basis. If you want something that happened previously to be relevant and affect the story, let it. If not, don't.
Episodic story telling is so downtrodden these days. I like gratuitous continuity as much as the next guy, but it's become so prevalent, I'm actually starting to miss the old loosey goosey style of story telling. "All that stuff happened before... kind of" works great.
It worked out great for the HULK. We can substitute in the TV show, only he wasn't called David Banner, and the new movie, only he was played by Mark Ruffalo.
It's something they should really try with the Spider-man movies when they finally get round to rebooting it. Origin story, Goblin, Doc Ock, Venom, Lizard and Electro. All sort of happened, but a little different. So Ock can still be alive, and maybe instead of going to an insane asylum, Peter kept the Lizards secret, and now they're besties.
Maybe even take it a step further, and assume that other villains and allies have already had stories. Opening scene could be Spider-man foiling Shocker as he robs a bank just to say, "this is the tupe of world where this happens and there's super dudes all over the place". Or Black Cat shows up, they interact, and let the chemistry tell the history.