MJ doesn't remember Peter Parker. But she kept his necklace and still feels something
That detail becomes significant when you understand what Jean Grey's powers did in the final act of Brand New Day.
Her powers at that level of force doesn't leave Doctor Strange's memory barriers completely intact.
She wasn't trying to break the spell. But she disturbed something that was never meant to be disturbed.
Ned's handshake proved it. His muscle memory responded to Peter before his conscious mind could stop it.
MJ is carrying the same evidence around her neck without understanding why it matters to her.
The spell isn't broken. But Jean Grey's evolution put the first fracture in it