Ry,
I would guess that you trimmed the walls to the roof. Trimming operations remain intact until undone. To undo the trim select the walls in question and open their Settings Dialog. Part way down (near the material in AC 12, not sure where in 14) you should see a button that is marked Unto Roof Trim. Click it and then click OK. Your roof trim will be no more. Reselect the wall and desired roofs and do the trim to roof operation again with the roof(s) in the new location.
While there is plenty of use for the trim to roof function, you may want to explore Solid Element Operations (SEO) as well. This will do much the same thing but the result is dynamic in that the trim location will move with the movement of the various elements used for the SEO.
Erich
AC 19 6006 & AC 20
Mac OS 10.11.5
15" Retina MacBook Pro 2.6
27" iMac Retina 5K