The two methods to do this are either (the one already mentioned) which is to convert that compound roof into separate single plane roofs (right click -> convert to single plane roofs) and then just subtract the affected area from each affected individual roof like you would a slab.
Method # 2 is to use SEO booleans and subtract the area using a hidden boolean slab or object to create that void.
The obvious problem with this method is that Boolean SEO operations don't show the correct result in plan view (unless your Boolean-ing Moprhs.) - which is a problem that Graphisoft have been really lazy to fix or correct ever since SEO's were introduced over 10 versions ago.
Theoretically the "Hole" tool might also work, but I don't use that tool too often myself, and have yet to gage how effective it would be in subtracting rood volumes and masses.
Perhaps someone else can comment on the viability of this method.
I would personally go with the first method, which, even though it explodes the roof (but you can still keep the individual roofs grouped together), sill leaves you with correct roof objects behaving as roofs and showing correctly in plan.
