So this has bothered me with the whole "time travelers immunity" thing. When Crono, Glenn, and Magus get back to stop King Zeal, the Reptite Timeline is avoided but the party is still sent through portals by King Zeal.
So obviously, another version of Crono, Glenn, and Magus are sent, thus creating two sets of them due to time travelers immunity. Can anyone say "Plot Hole"!
I know the CE team obviously missed this little mistake, just like how you guys forgot that destroying the Dragon Tooth, failed to solve Chronopolis' energy problem, forcing you to fix that in a sort of corny way, even though it was completely destroyed along with Sorin (even if Chronopolis reconstructed it, that's kind of stretching it...).
So, care to comment on how this could be resolved without the entity/planet negating the other party. Imagine them being abandoned and having to live out their lives and die knowing they can never get back, always wondering what could have been and happend to the timeline...
There is no plot hole, actually. When Crono, Glenn, and Magus return to the moment they were sent into the "Reptite Timeline" by Zeal, they had not yet acted upon disrupting Zeal's spell. At that moment, there existed two possible destinations for Crono, Glenn, and Magus to arrive - one was the non-reptite destination, and the other was the reptite destination. Originally, the non-reptite timeline was sent to the Darkness Beyond Time, because that timeline was eliminated, leaving only the reptite timeline. Now, when the three return to stop Zeal, they send the reptite timeline to the Darkness Beyond Time as well and "restore the timeline." The thing is, they really didn't restore the original timeline but instead created a brand new one that was very similar to the non-reptite timeline. What happens is, as a result, the Crono, Glenn, and Magus that were sent into the portal right before the versions who returned and stopped Zeal were sent to the Darkness Beyond Time. In the end, we still have Crono, Glenn, and Magus around with their memories due to Time Traveler's Immunity, and the versions of themselves that they witnessed entering the portals were sent to the Darkness Beyond Time. That doesn't hold true for Marle, Lucca, or Robo because those versions o themselves in the reptite timeline were sent to the Darkness Beyond Time, but the versions of Crono, Glenn, and Magus came from the reptite timeline and were not sent to the Darkness Beyond Time. Since they weren't sent to the Darkness Beyond Time, new versions of themselves in the new timeline they created could not exist and were sent to the Darkness Beyond Time.
It's all very complicated, but it does work out.