What I will do with those punchouts of my KS case, is to drill one or two holes in the center. Here I will first make dents with something sharp, this is to prevent the drill from wandering off. Then I start with a small drill first (3 or 4 mm), and then gradually increase the size until the hole(s) are big enough so that some pliers can be used for carefully ripping out the remains (perhaps with the help of a sharp knife). By now the structure of the punchout should have weakened enough, so that doing this would go without any issues.
After this is done, I will use some small files for cleaning up the edges of the hole.