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In the events of Amazing Spider-Man #Brand New Day and after it becomes clear, that Peter somehow erased the knowledge of his secret identity from literally everyone. Neither villains nor heroes know who Spider-Man is anymore. In #590 Johnny Storm realizes he used to know Spider-Man's identity, but can't remember that. Spidey later (#591) explains to Reed how this all works.

Spidey explains "Psychic Blindspot" in #591

However, MJ still knows his identity. There's a hint in #559-561, where she talks to him over PA and says that they met in another life.

#561 Spidey and MJ talking over PA

Later in #601, when Peter and MJ agree to meet, but she oversleeps and misses it, she watches news about Spidey and knows it's Peter.

#601, MJ oversleeps #601, Spidey news #601, MJ knows Spidey's identity

If everyone's mind has been swept off, as Peter points and explains to Reed, how come that MJ still knows who Spider-Man is?

As per @Shreedhar comment, this clearly implies MJ thinks that Peter talks himself up by talking Spidey up.

MJ calls PP narcissist when he talks about Spidey


Click all images in the post to enlarge them.

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    Its possible that she doesn't know PP is Spidey. Because MJ does call almost everyone as "Tiger". At least I've seen in the next issue (# 602) her calling Harry as tiger. Moreover, in the same issue she talks to Peter (who is actually the Chameleon in disguise, issue # 603) about Spider-Man as a third person as if she doesn't know him at all.
    – Shreedhar
    Sep 19, 2019 at 9:23
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    @Shreedhar actually she calls Peter\Chamaleon narcissistic when Chameleon tells her about what Spidey did, actually unaware that he's posing as Spidey's secret identity Sep 19, 2019 at 9:25

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This is all explained in the One Moment in Time story line which recounts what happens: why they never got married, how Aunt May was saved and how Mephisto actually changed the timeline. Effectively all he does is allow a criminal to escape which sets a spiral of events in motion as we see in Amazing Spider-Man Vol. 1 Issue 638.

The criminal escapes the cop car in 638
Click image to enlarge.

This all culminates in that criminal going after Aunt Anna, MJ and MJ's family. MJ is knocked unconscious from a blow to the head in this and Peter takes her away to Strange. Once there he asks Strange to wipe his unmasking from existence. Strange meets with Tony Stark and Mister Fantastic in the Astral Plane to do this. This all happens in Amazing Spider-Man Vol. 1 Issue 641.

Strange and Mister Fantastic discuss the process with Tony
Click image to enlarge.

During the process Peter is to be sealed away and protected to be the sole carrier of the knowledge. However, he leaves the cocoon and takes MJ in with him so they are the only two who know Peter's identity. So in short MJ never has her memory of who Peter is erased.

Peter leaves safety to take MAry Jane with him The process is shown to complete with only Peter and MJ in safety
Click images to enlarge.

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