Your roof shouldn't change because of the hole. The roof should refer to the top of your walls so 1rst, your roof is on the main floor plan and not the basement?
If it's on the main floor plan, then your heel height should be negative to show as it is. Did you modify that? You may need to correct your TOP to Fascia Height under Soffit/Fascia.
When in roof mode, 1rst do a cleanup. Then, make sure that the bubbles (lollipops) refer to the walls. Sometime you have to move them a bit to activate.