You cut it out with Combine2. The common area occupied by both bodies is what remains. Since the flat raised surface is outside of the other body, it's removed by the combine.
My only guess is that the parent/child relationship between Combine2 and your FLAT RAISED SURFACE feature are based on body selections rather than surface/faces/vertices created by any one feature.
You cut it out with Combine2. The common area occupied by both bodies is what remains. Since the flat raised surface is outside of the other body, it's removed by the combine.