Sounds like it may be getting accidentally parented. Try selecting the empty and the planet surface, and then press ALT + P > Clear Parent.
If that doesn't work, let me know and we can try to find a different solution!
Didnt work. I closed and opened, deleted surface and rebuilt. Then noticed that when I moved layer two by accident it affected layer three a little. Started to look around at UI options and discovered I had apparently hit "O" by accident and turned on Proportional Editing. All works as expected now. Thanks for your help.