First of all, sorry for a bit of confusion there. I used an argument that probably wasn't the most fitting for this case. I'm currently in the process of devising a comprehensive theory governing the laws of time-travel, which would dictate that in this case, the "new" Magus would survive. Let me give an example of how the Time Bastard theory wouldn't quite work out, using a possible instance of CT, and a few extrapolations:
Crono is in 1000 AD, with the charged pendant. He goes to Porre village and sees two black chests. He grabs the treasure in the first chest, but leaves the second alone. He travels back to Porre in 600 AD and sees both chests again. He again grabs the treasure in the first chest, and powers up the treasure in the second chest. He returns to Porre of 1000 AD and sees that only the second chest is there, with the powered-up treasure. Obviously, his actions in 600 AD have affected what he sees before him.
Start Extrapolation: Crono asks a resident who's been watching this room in 1000 AD what happened earlier. The resident looks at him funny, and says, "Well, you came in, looked at the chests, and left." No mention of the fact that he took the treasure previously, as he didn't in this new timeline. He's hearing a tale of what the "new" Crono, created in this timeline, did. What happened to this "new" Crono? When he traveled back to 600 AD, he coincided with the old Crono, and was sent to the DBT.
The point of this comes when one considers all the previous jumps Crono made (or could have made) before he arrived in 1000 AD at the beginning of this narrative. All of these actions would have been rewritten for the "new" Crono once Crono changed something in 600 AD. In this case, the "new" Crono took precedence over the old Crono in all jumps leading up to the "old" Crono's arrival in 600 AD in the middle of this narrative.