Thanks for updating your profile.
You are running into the tiny face issue. Since you are using groups in your model, I scaled the whole thing up by a 1000x and then successfully subtracted to get the counterbore. If you use components instead of groups you could do this using the Dave Method.
How do you plan to use the model? Is this for 3D printing?
It looks like there’s a lot of unneeded triangulation in your large group. I expect if you were to clean that stuff up first, your model would be easier to work with.