I started a scene with several hi-res terrains, added a couple complex objects via "merge" command, then I added a third object within the scene. 

This third object was started by flattening a sphere considerably then duplicating it several time and moving each duplicate slightly.  I applied a mat and started a test render.  All is well so far.

I save the scene.  Then do another test render. 

Upon starting the render the object made of flatten spheres transforms itself into multiple perfectly round spheres.  The mesh is correct before starting the render but that transforms also.  Go figure?

Bug strikes again.  I think I may resort to good ole Coreal Bryce 5 except for hdri.