In the cut-scenes of the Wings of the Goddess mission 'Maiden of the Dusk', Lilith tells Lilisette that the two timelines can co-exist if Atomos is sealed away from both ends, so as to avoid the timelines from conflicting.
Before Lilisette crosses over to the world of strife, she asks you to help her do this. She will seal off the maws, and so will you. Then they will, over the course of decades, turn to stone and stop working.
But, it's never explained how we are meant to do this? And because the missions end shortly afterwards, we're never actually seen to keep our promise.
Did I miss something, or was this never explained?
If anyone could shed some light on this, I would greatly appreciate it.