You may notice that sometimes a subtractive brush cuts into one additive brush, but not another.
This is because brushes are order dependent, they're like a set of commands such as
Build this, Now cut into it, Now build on top of that, which are shown in the following screenshot:
If we want the subtractive brush to cut into both the additive brushes, we can make it the last command in the list. Select the subtractive brush, right-click on it, and select Order | To Last.
Now the brushes are in the order we want.
And if we rebuild geometry, ...