Welp we know that Jean is still alive (she just wandering around finding pieces of herself) and that for a short time in "Endsong" Emma was in possession of the Phoenix Force for a short time.
And that Jean...in a small way allowed Scott and Emma to get together post her 'death'.
So it would make sence that Jean...being a cosmic entity would have a way of watching her friends, similar to how she gave Scott permission to find happiness with Emma as opposed continually mourning her, she might be giving Emma the tools needed to save herself and the others.