There is currently a compatibility issue with the AU version of Auto-Tune® Pro and FL Studio on Mac. The problem that occurs is when you reopen a session, Auto-Tune Pro will revert to default settings even though you saved the session with your changes.
To work around this, please use the VST3 version instead. In FL Studio’s effect window, you should see two entries for Auto-Tune Pro, one for AU and one for VST3. Be sure to select the VST3 version.