I don't know how others handle this but I use the generated roof-gen level to save the room that was used to create the roof. After generating the roof I move it like you did to the correct level and move the room that was the source to the roof-gen level (after naming it). Then I make the roof-gen level unviewable. That way the source-room is saved for a possible re-generation without interfering with the rest of the plan. With multiple rooms/roofs I just collect the rooms on that same roof-gen level en delete extra roof-gen levels that appeared.