After episode 311 there was a TVline report in which A and E clarified that Mal wasn’t the Black Fairy and that we had never seen the Black Fairy before. Now, they could go back on that if they wanted, but it is out there.
I think that was just A&E treading water, because back in 2013, it was unclear whether the actress who plays Maleficent would be available again to reprise her role. Now that Kristin Bauer van Straten is free to return to the show, A&E may very well change their tune and make it seem like the dark fairy was always meant to be Maleficent.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy