[spoiler]It was never said that she died, only missing. And all throughout CT, Ragna was just [tornado fang]ing people up. He wasn't exactly fighting to avenge Saya or searching for her.
Ragna himself even suspected that it was Saya behind this from the very beginning.
As to what happened, basically When Saya took over/destroyed the Master Unit, she ended the time loops. And thus the Continuum shifts. As she put it, the past stays the past, and the dead stay dead, (PEOPLE DIE WHEN THEY ARE KILLED!!!)[/spoiler]
This of course causes Hakumen to now be a Time paradox. As in this final time line that didn't loop, Jin no longer gets fused to the Sanshinkin unit by Rachel.