Doesn't the Mephisto effect make it so that not only do they not know Spidey's identity, but the don't even know they ever knew? In the FF issue, didn't the FF only realise something was up when confronted by direct evidence (a statue of unmasked yet faceless Spidey with the Four)?
Not that I'm defending BND, it still blows a wide variety of chunks. But is seems that under what little logic they have so far about the identity thing, Felicia might not even remember she ever knew, and therefore not care about about who's under the mask. And if that bit of Felica's character development is dependant on her knowing Spidey's identity, It seems logical that erasing that knowlege would cause her to revert.