I believe one difference in moving to Region FX is that V-Vocal no longer leaves the original clip in place after processing the clip. V-Vocal is a DirectX effect and on the wane, so the program is adapting to Melodyne's preferred method of working.
scook's comments in post #3 are correct. Studious's comments in post #4 are correct for versions prior to X3.
The workaround is to process a copy of the clip if you want to keep a safety. If I'm going to apply V-Vocal to a track, I clone the track and archive the clone. If I reach the end of the project and I'm happy with the V-Vocal track, I usually delete the clone.