
Basic consensus is that time traveling beings have time travelers immunity (i.e.
Chrono compendium has whole articles on this. While unlikely to be stable, such a world has a non-zero chance of occurring as long as the Balthasar-Future thought the Time Devourer could exist. El Nido's existence was due to the Time Crash, which occurred because of FutureTech experiments in a world where Lavos was defeated on a Lavos fragment. Remember kids, even dimension hopping is not safe from the Timey-Wimey Ball. We're dealing with what happens after the Time Devourer was stopped from the perspective of the timelines that are aware of it.but since, depending on how you view it, it exists either at every point in time simultaneously, or no point in time at all, its defeat means not just the cessation of its existence, but the nullification of it having ever existed - its pocket dimension exists outside the flow of time, so there's only a constant "now" in which it no longer exists. We're dealing with travel between timelines, not up and down a single timeline. And the Grandfather Paradox doesn't really apply, here. But we briefly see Serge in what appears to be El Nido at the end of the game. Maybe it doesn't? Maybe the scenes in Other Schala Kid in the modern day are the rewrite of time? Of course, if the Time Devourer never existed, then nobody would have stopped it, and there we have the old Grandfather's Paradox.
how does El Nido still exist, as it only comes into existence due to actions by the Time Devourer?
This eliminates the possibility of Serge being absorbed by it, and thus the potential for his nullifying the death of Lavos. Okay, as far as I can tell from in-game content and external sources, the game ends with the Time Devourer having never existed, as the Chrono Cross undoes the Fusion Dance that created it, and it exists outside the normal flow of time.