I have found that doing the cleanup on the 2nd floor does not always work by itself to fix the problem. I have also had to do a cleanup in the 3d view after doing a cleanup on the 2nd floor plan (or whatever floor the roof is on). Sometimes that does the trick. When that doesn't work I have had to restart the program. Sometime after restarting the program the roof will still come in all messed up. I then do the cleanup on the drawing that has the roof system and also a cleanup on the 3d. That has never failed yet.
When that does not work.............