Remove at request thank you.

I've had weird issues like this before, there can be multiple reasons for this to happen. I don't know what your issue is exactly, but here's what I've done to fix similar problems.

Make sure you have a reflection probe/probes set up correctly, covering all interior geometry. Check your skybox and make sure you haven't accidentally deleted one of the six brushes. Also check the umbra volume, the sun volume, and also don't forget to build and then export the lighting within radiant. If there is any geometry intersecting the faces of the affected brushes, sometimes this can cause the faces to either not draw or flicker intermittently, because the textures are fighting to be rendered at the same location.  I would select each brush that's fucked up and hit S (in radiant) to bring up the surface inspector and check the texture settings or just tweak them. It's also possible that you didn't assign a texture to all of the faces. Again I don't know if these ideas will fix your problem, but usually those problems are derived from lighting inconsistencies, at least in my limited experience. Hope this helps man, good luck.

*Oh and more thing I just thought of, are you using any lit_advanced textures, or any similar materials? Those types of materials have extra texture channels that calculate light interaction with the surfaces you apply it to. In that case, given that you also have not built the lighting in radiant, and have not built lighting in launcher, those textures won't render in game. I've had that specific issue before and resolved it by just building the lighting and re-compiling. Also, some of the available textures in radiant are just gimpy as hell, and will not render properly period in some circumstances, usually rare but to check for sure, hit f8 in radiant, build the lighting, then inspect the surfaces to see if it's fixed before re-compiling everything. If nothing else, change the texture to something that you have working on another surface, and then re-build and check again.

*EDIT - I can tell you haven't set up reflection probes, just by looking at the light bleeding through the corners, and at the top and bottom of the interior perimeter, at least that's the way it appears from the screen shots. You can set up shadow/sun caulk brushes on the exterior to help eliminate the light bleed where necessary as well. Also now that I think of it, try ditching the thicken brush or whatever it was you mentioned at the affected brushes, any intersections there may be inadvertently causing the issue. In any case, let me know what you end up doing to fix it, I hate these problems lol, I know how frustrating that crap is. Im curious to find out.