Won't copying CMod's folders over Maldo's overwrite the latter's "levels" folder? I thought most of Maldo's fixes (tesselation, flickering geometry, misplaced textures etc.) were contained in the individual levels folders.
Just had a look in the CMod levels folder and I see that he only has the Level.pak file in each folder so those will overwrite Maldo's. Wonder if Maldo or CMod fixes are contained in those particular files. Also, wonder if CMod requires the levels folder to work, otherwise we could just skip those.