I know this is an old question, but meshes are a weak point in Archicad's toolset - they do not participate in material priority intersections, nor to edges in plan clean up like with slabs. You're stuck with solid element operations, which don't work follow renovation filters. In general it seems that many people just use entirely different meshes for each phase of work.
I found that the new opening tool does work on meshes - you can simply set one down on the surface of your terrain, shape it to the building footprint, set its renovation status to new, and it will at least show a cut, but it won't help will fills, and scheduling isn't accurate either.
