I don't know, there's some amount of interpretation here considering how short the ending we have now is, but us going back to the dawn of times is also what manifested the Akashic record itself. Xion is pretty clear about the dilemma here:
"... However. However. Even were we to lose the history stretching from past to present... The future must not lose you."
And then later, to Matoi
"It would deny history... the Akashic Record... a denial of my very existence..."
With that being said, had Xion never existed, most of the plot of this game obviously couldn't have happened the way it has, so either there's more to it, or the writer's version of time manipulation is that she stops existing the moment actions that erased her happened(so at the end of EP6), or something.
Regardless, in all honesty unless they give the characters in Omega a way out, I can see the argument that they wouldn't erase it. They're clearly going for a good ending here, and that would kinda just suck.
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