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"!
Not a plothole. The original Crono, Glenn and Magus stay X days in the Reptite 1005 AD before returning to Prehistory. When they change the timeline, versions of Crono, Glenn and Magus still emerge in 1005 AD due to TTI, but they
fade from existence after X days. This is due to the concept of Time Bastard that the Compendium deduced from CT (Melchior and Janus) and CC (Ideal Timeline Serge):
http://www.chronocompendium.com/Term/Time_Bastard.htmlBasically, the "duplicate" versions of Crono, Glenn and Magus aren't duplicates at all, they're just the
past versions of Crono, Glenn and Magus ("past" in the sense that they are X days younger than the player's version of them).
You might think it's odd that some versions of them spent X days out there before disappearing, but it happens more often than you think in CT and CC. For instance the player's Crono grew up in a world in which there was no Fiona Forest, but there's also a "duplicate" version of Crono who grew up in a world in which there WAS a Fiona Forest. Crono's Mom lived with this "duplicate" version, but he disappears in 1000 AD and the one that returns is the player's version, not him. Kinda creepy, eh?
There was a lot of interesting discussions on alternative concepts in the recent months; I don't know if they're "better" than the current concepts (I haven't had the time to read them yet), but CE is based on these TTI and TB.
EDIT: lol Acacia Sgt and IAmSerge beat me to it pretty well.