I just tried to recreate this problem and could not. I picked a NEF file and did a soft crop with PM. I saved a copy of the file for the "before image" and then edited and saved the original a couple times with NX2. The soft crop is still there. I tried changing the star and color rating with NX2, making a change in the develop section, adding an edit step and loading presets. The soft crop was still present in the updated image file. I even tried doing a crop in NX2, and the PM soft crop was still there. The NX2 crop did not change the aspect ratio, so the soft crop was still the same size relative to the entire frame.
I know it has happened to me in the past because I was quite disappointed when I lost the crops. I simply can not recreate it any more. I'm pretty sure I've had at least a couple updates for PM and possibly an NX2 update since I remember experiencing this problem in the past. Maybe something in the updates fixed this problem.
Danny