1. Did you render the Melodyne audio track? If not, there are many functions that can't be performed on it. I assume a punch-in is one of them.,
2. Did you look in the take lanes to see if there is indeed a new and an old take? If so, mute the old melodyne one you don't want and listen to the new one.
3. If it didn'r record, just record on a new track and cut/paste it into the old file later. Use a clip envelope to silence the part of the old track you dont want to hear during recording.