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Also, NEVER clip or carve something with indicator lights on it. "Accessed Deleted Entity. Tell a programmer!" Nothing big happens...except that every lidlight on that section has the Brush Face field cleared out. 
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Just, never, carve.
As for the clip part, it's perfectly fine to cut something with indicator lights on it! The thing is that your brushes won't have the same brush id's anymore. Basically, if you'd have a box say 128x128x128 inside you have 6x6 faces. Since you need 6 brushes to conceal the block, and each brush has 6 sides as well.
We created those brushes first so basically face 1-36 are taken.
Now we apply an overlay (like indicator lights) to face 4. (this means brush 1) if we cut this in half we suddenly have 2 brushes, rather then 1. So 12 brushes rather then 6. This means that all sides get a new number, since there are two new brushes. To prevent errors, hammer continues after 36, so our two new brushes will get the face id's to 48. (Note that 1-6 are empty now)
Because we applied the overlay to face 4 and it's gone now, the overlay does not show up again. The easiest way to fix this is to select the overlay, open the overlay's properties and go to "Brush faces..." and then use the "pick" button to select the brush face where the overlay is on and it shows up perfectly again!
Nope... there is still another way if the overlay is already placed on a brush surface that has been clipped: open the overlay's properties and go to "Brush faces..." and then use the "pick" button to select the brush face where the overlay is on.
useful tools and stuff here on TWP 
[spoiler]
[/spoiler]Nope... there is still another way if the overlay is already placed on a brush surface that has been clipped: open the overlay's properties and go to "Brush faces..." and then use the "pick" button to select the brush face where the overlay is on.
sorry, I re-phrased this the wrong way. Your method is absolutely the easiest way to fix this.
I know how to use a hammer and a screwdriver, but that doesn't mean I can build a good house hehe
Aren't you forgetting a saw and dirt moving tools? Housebuilder pfft
That is four spheres carved into each other. The blue lines in the 3D view are the edges of visleaves.
I see what you did there UsCubra11.
those kinds of visleafs would probably happen with 3 spheres anyways.... func_detail everything.... and aslong as you only are making 1 clip into a brush, its really no big deal
but it is still a bad too, and shouldn't be used often
I've been using the carve tool to make sqaure holes in the walls to put my door and boxdropper instances into. I thought that wasn't too bad for visleaves and such? I could use the clip tool as well, but it takes longer and gives the same result.
What I think is that it does NOT give the same result. If you obtained the same result must be only by coincidence. As said above the carve tool algorithm makes many unecessary brush pieces... Please check the attached door frame I made by clipping and using the vertex tool. Whenever the carve tool could be remotely useful, the vertex tool, altogether with the clipping tool, will get over it by far 
useful tools and stuff here on TWP [spoiler]
[/spoiler]Sorry, I mean just to make a square hole. I have an instance using the clipped-up door frame from the zoo_mechanics file, I just needed someplace to put it.
Carve gave me two pieces on the sides, one on the top, and one on the bottom.