Flashes Before Your Eyes

So I am doing a rewatch of the entire series and just finished watching "flashes before your eyes". This is going to be a pretty vague question, but can someone explain exactly what happened to Desmond when he turned the fail safe. In Season 6 when he gets blasted with the electromagnetism, he becomes aware of the afterlife timeline but in this episode when he turns the fail safe key, it appears that he goes back in time. So just his conscious went back in time right? Why does he go to the afterlife in season 6 but in this episode he goes back in time. And how does Eliose know what is going on? Im a little confused here. Someone help me out if you can.

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