Hi there!
Just experiencing the same issues as you. I discovered that renaming my project file (just a save as adding a ‘ver 2’ for example) sometimes seems to cause melodyne data loss - exactly as you show. I wondered if you could test doing a save as on a similar project.
I too have opened a support ticket and have been waiting months for a reply with no luck.
I also have issues using tape machine style monitoring with ARA2 and melodyne - Have you tried punching in manually recording on a track that has events melodyned already whilst using tape machine monitoring option? Heres a video on it. https://youtu.be/IByNB5Xb0Vs I have done a separate support ticket for that too.
Here is a link to my post on the issue Thanks!