I have the Antares Auto Tune EFX. I had asked about it's use, on here, and the suggestions (which I have taken) were to use the Auto Tune by itself and then bounce the track (to a new track) and then do whatever else you want to do or add to track.
I don't delete the original track (with the Antares) after I do the bounce. I mute the track and keep it, "just in case".