It's not hard to think of how this might play out. Story spoilers to follow

When you consider that the Source was split through the acts of Hydalyn, and we know that the next expansion will be concluding the story of Hydalyn and Zodiarc to pave the way for a new story to come, if we were to eliminate the two elder primals from existence, it's possible that the worlds as they currently exist cease to be. Yes this will make all the work we did to save The First completely irrelevent, but there could be a rebirth of a newly combined world that has places like Eulemore and the Crystarium superimposed into the Source. But this also could take place through less violent means than a full on calamity, something like the combination of worlds in FFV.

Considering FFXIV is a playground of sorts with references and story beats lifted from other Final Fantasy games, this also would be a story beat similar to what exists in Dissidia Opera Omnia where the destruction of the crystal cores of light and darkness causes the world to be destroyed and reborn.

A full reset of the world like this could also pave the way for them to reset character levels as well, though considering they're going through with a stat squish next expansion, this is unlikely.