While testing this issue it was interesting to discover how the surrounding BSP's were affected. They seemed to clip/disappear according to the surface normals of the deleted brushes.
There is a simple workaround to convert your bsp's to static meshes after modifying the faces, and the surrounding brushes reappear and render as expected.
1. Open attached project.
2. Toggle Geometry Editing (Shift+5)
3. Select one of the larger faces on the long BSP brush.
4. Choose the 'Flip' option.
Outcome The surrounding bsps relative to the surface normal of the flipped face become invisible or get clipped.
Expected Only the bsp being edited should be affected in the viewport.
Head over to the existingAnswerHub thread and let us know what's up.