White Wolf seems to be the grand-daddy of metaplots.
In Vampire, after a certain point, one of the Clans was all dead. Which, in D&D terms would be like saying, 'Okay, due to story reasons, you can't play Rangers anymore. They all died and we won't be releasing any more books supporting them.'
In the Scarred Lands setting, the Elves were 'forsaken,' their diety having died in a war, and been expunged so thoroughly from existence that his *name* was forgotten, even by the elves! In the metaplot, he came back, as a result of some powerful NPC doing something. I have no idea, I never read the novel. My game was set in Hollowfaust, which, last I heard, had been blown up and destroyed. I have no idea how, but it's, IMO, the coolest darn city in the entire setting, and even if they hadn't cancelled the line, they made it clear that they weren't publishing any support for people who used it anymore.
I could care that a particular class / diety / whatever gets kacked off. I don't like that I'll never have official 3E Domains for Lleira in the Forgotten Realms, because some poorly-conceived and inconsistently written novels killed her off-stage in a single sentence that can be paraphrased as 'The uber-cunning goddess of deception, lies and trickery was invited into a dark alley by the dude who had just killed the god assassination and stolen his power, and, I guess he had candy, because she went alone and unprepared and got herself assassinated and devoured.'
It sounds like some munchkin's power fantasy. 'I say to Thor, 'Psst, C'mere' and he does, and then I grab Mjolnir and push him off a cliff!' But apparently it's canon, and there won't be an Initiate of Lleira feat anytime soon.