Hi I have been struggling with this in Cubase 11. For anyone that is interested please see Melodyne LOSING all pitch edit data when doing a save as OR Cubase saves a new version
Things that corrupt melodyne over ARA 2 for me are;
Disable an ara extension’d track (May recover if enabled immediately after but often a few saves later and the data is missing)
Track Visibility (Tracks will dissappear in melodyne side bar then become uneditable)
Track Versions (this can cause corrupt data after saves or confuse melodyne)
Save as (renaming the project under a different name - even adding 1 character)
Hope this is helpful
Ed