Using Melodtne Assistant, latest Version.
Add a vocal track and copy and bounce the new vocal so it is a separate audio file.
Now add the Melodyne Extension to both tracks.
Audio timing is altered resulting in-phase/flanger effect.
Now save the small project, CLOSE and reload.
Phase/Flanger effect has gone, audio is back on time.
Submitted to Steinberg but wondered if anyone else could test.