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Never heard those rumors before. That is misuse of the Chris Carter Effect though, as it seems to imply that people thought these plots would be followed up on, whereas in the Chris Carter Effect, they become convinced that no plot thread will ever be followed on and lose interest. If they had lost interest, as you point out, there would be no Fanfic Fuel, etc, as most viewers would have had any will feel anything towards the show drained by that point.
It's misuse since they are applying it to one shot characters that never became complete Ensemble Dark Horse.
My Little Pony: Friendship Is Magic
I think this is misuse as The Chris Carter Effect is when audiences lose interest because it never resolved its plots. This is not following up on it’s plots, a separate issue. And if they were this “ by the end of Season 9” the series finale, it’s misuse as they would have stopped caring before the work ended.
And this is the first I’ve heard the rumor despite following the mainstream fan-sites. Is this the sort of accusation that needs something more substantive than rumor?