Missy probably knows what's happening because she's experienced it before. We never see Simm's Master regenerate so we don't know the circumstances of how he became Missy.
You can take it with a grain of salt but when Missy and the Doctor first meet and she clues him in on who she really is, she says that the Doctor left her for dead.
That's not how they've established multidoctor(master) timelines to work. Only the most senior one has memories of the events and only after they've experienced them.