If the new deep is completely empty, it is NOT a brood nest. It is empty. It is currently nothing.
Yeah, that is what I am thinking.
The super is on top the new box.
I would slowly disassemble the medium right in front of the hive.
Are you not telling him to disassemble the box that has the brood in? From his description, I envision a hive that consist of a medium (brood box) and a shallow honey super on top. I believe he claimed that he can't get the bees to move down into the deep so there is nothing there. Please correct me if I have this picture wrong.