They edited the original derpy voice because somebody found it offensive. I'm not sure if it was the general populace (doubtful) or one really pissed off media icon? Or maybe it was a writer? I dunno.
They didn't remove her, but her new sound-clip removes the 'implication' that she was mentally retarded.
If you ask me, I say anyone who thinks that the original derpy voice was offensive is ignorant. There's nothing wrong with having a 'mentally challenged' character in any media, unless you're blatantly bashing the fact that they have a mental disability, which was not the case here. The fact that they changed her voice is just an insult to mentally handicapped people everywhere IMO.
I love Derpy, regardless.