Guess it's just down to a difference in opinion since if she removes Kyon 1 she doesn't save all versions of him. Like I said I prefer the thought of Kyon 1 being somewhere else in the timestream and have a role in a story further down the road.
Edit: Just thought about something about my own question. If the first one went through the altered world and became the "second" one there's not really any rule that says the second Kyon had to be taken back to the same day he left. Nagato could basically have programmed his actions for the day and have him fall down the stairs and with this method she wouldn't need to "erase" any Kyons at all.
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