We have new information on the nature of the clones, which puts what Twilight did to them in a whole new light. And you know she WOULD hunt it down and kill it if she knew it still existed.

Logical explanations people have come up with in the description that I liked (I still like mine the most though!):

1) The Law of Conservation of Ninjitsu could be at play here. When there are a lot of Pinkies, they are all just shadows, but when that is reduced to one, the remaining one slowly gained consciousness. (Though it’d still be terrified of Twilight if it’s smart).

2) One of the original clones though a balloon or train or something looked fun and hopped on, ending up in Manehattan, and never ran out of fun things to do there enough to go back. It gets scared and leaves due to overhearing Pinkie talk about the terrifyingly unfun thing the others had to do. While the clones probably wouldn’t take good care of themselves (like bathe and such), someone else could be taking care of it without knowing that it isn’t a real pony.

I’ll post more good explanations if someone else comes up with another. Linking tvtropes is always a plus!