I would also like to take the time to point out that ChrisX will not be returning. Particular... sensitivities were run raw here, or so I heard, and he does not foresee an improvement if he were to return.
Anyway, back to the topic at hand - speculation on the story of Chronophantasma. I'm not surprised everyone's focusing on Ragna, given how the focus of the story has been on him all this time. Nor do I doubt he or the others may find a way to overcome this particular setback, however temporarily. But my eye has glossed over that, and is instead focused on other points which may or may not help resolve this one.
A] Given that Noel and Tsubaki are themselves and back together again, one is left wondering what role Makoto has left to fulfill. With Relius having lost his plans and much of his motivation (outside of restoring Ada so he can face his judgment), his "random and untoward" interest in her is left unresolved thus far. I am not oblivious to everything that has been hinted - in addition to the aforementioned, Arcade commentary from Mu (CS) and Nu (CP) both note her resilience to seithr (an early translation from Nu's commentary brings up a 0.2% absorption rate), and Hakumen and Valkenhayn both had positive things to say about her (considering how hard Hakumen is to impress, that says a lot). On top of that, we know almost jack about her pre-Academy life, but from what has been gathered in CS, if being forced to relive it broke her in record time (see the bad ending), it wasn't pretty... not by a long shot. I have this feeling her role in affairs is much deeper than we are allowed to perceive.
B] Thanks to certain parties attempting to divert my gaze, I have to wonder about Litchi as well. With the world's seithr having been neutralized, I don't think Arakune has much time left either, so if he is to be saved, it had best be soon. Given we do know that Carmine (I am using his last name to avoid translation inconsistencies) became what he is due to tampering with the Boundary and the Azure, any method that could help him might extend to saving Ragna from his out-of-control Azure Grimoire as well. Operating word: might.