But they also appear on Opassa Beach in the True Timeline when you go fight the Devouer of Time...
Crono mentions that Lynx and Harle tried to capture Lucca to disengage the Prometheus circuit but the mission ended in failure... but it never mentioned she was killed. Was it as Chronopolis that it's mentioned?
Also... Lucca says that "they" (Crono, Marle, and Lucca) no longer exist in the main timeline. I'm guessing this can be interpreted as them being dead... yet the three "ghosts" talk as though they are the originals instead of alternate versions of them. I'm just saying that when we are dealing with a game where people can time travel and travel through parallel worlds, saying "..we no longer exist in this timeline..." doesn't necessarily mean death...
Conspiracy theory...