I can tell what piece of dialogue you’re referring to, and yes that is in reference to Black Doom’s time anomalies, not Time Eater’s erasure of space-time.
“If we can resolve THIS crisis, we will return from whence we came. Space-time will settle as it shifts back into place, like rippling water becoming calm again.”
Gerald only knows of the situation with Black Doom as evidenced by him referring to it as “this crisis” and saying “WE will return from whence WE came.”
Further evidence is in the way he describes the situation. “Space-time will settle as it shifts back into place, like rippling water becoming calm again.” If he’s really referring to the erased cosmology, what “rippling water” is he talking about? There is no “water” to become “calm again” with space-time erased, it just doesn’t make a lick of sense if he’s referring to the erased cosmology.
Now, take that same sentence, but apply it to the time anomalies created by Black Doom. Starts to make more sense does it not?