System Editor Guide

I've had an issue on planets with CSG symmetry where I'll delete a particular brush, but the mirrored copy that was linked to it will persist. Since mirrored brushes are unselectable, there's nothing you can do (for now) to remove it without editing the file.

It can be funky sometimes. If you've got to get rid of a metal spot, put a brush on top of it and toggle metal editing; that should delete the mex from under the brush. Something like a volcano would be good for this - it'd be tall enough that you could still select the above-water part to delete it once you're done.