Way to retrieve Melodyne tracks?

Did the tracks you opened in X3 show and play the missing parts?
Did you authorize your X3 copy of Melodyne on the computer you are using CbB on?
If you changed computers you have to de authorize Melodyne first.
 

The original (non-edited) audio file should still be in the Project Audio folder, which is the worst case fall-back.
 
First, try a reset and rescan of your VST plugins, that may solve it, but if corrupt it may not.
 
To recover the Melodyne edits (they are stored in the cwp file itself, so the Melodyne "Separations" folder content is not needed... Melodyne will reconstruct itself when the cwp is loaded), you may simply need to reinstall Melodyne. I recovered my computer from an image recently and Melodyne made me re-authorize it by deactivating the same machine (sort of funny). If corrupted, you may need to uninstall Melodyne prior to re-installing, then re-activate it on your machine again. If CbB fails to load it, focus on recovering Melodyne first. You may also need to ask Celemony what is up with the installation if the above won't recover it for you.