When opening an existing project that already has Melodyne you lose the transfers and editing that were done. Even though the VST is still in the FX bin nothing is loaded when you open Melodyne. I imagine it's because it's now using the VST3 version of Melodyne, but I would think it should still work like it did pre-ARA. It's not a big deal as you can turn off automatic VST3 use and then the VST2 Melodyne will be loaded when you open the project and work as expected, but it would be nice if you didn't have to do that. May be a Celemony problem and/or Calkewalk problem but initially it's rather scary seeing no data in Melodyne when you load an old project in X3. :)
Dan