Kaylockhart

Using room ceiling heights to change your roof only works if you have Auto-Rebuild roofs turned on, or if you go into your Build Roof Dialogue and select "Build Roof" each time you make a change. But in this instance, you'd probably want to open the roof planes themselves to move them up or down, since you have set ceiling heights within the plan. There is a relatively easy fix- you need to open up the main room on the second floor, and make sure everything in your Structure panel is set to "Default"- in other words, check all the Default boxes. You'll see the windows go back to normal and the ceiling will no longer be so high that it hits the roof. Then if you still need to make adjustments to the roof, open the roof planes themselves to edit their location, not the room ceiling heights.

I stopped at 22 items, using the Base Cabinet tool.