I have no idea what you think these configuration files are doing, but they're not doing it. It almost seems as if you think a compiled exe is dynamically recompiling itself according to some arbitrary file you have laying around.
Config files are just text files. You read them with ReadLine and ReadFile and you write them with WriteLine and WriteFile. What effect they have on the program is entirely up to you, which is to say you have to write the code to read them and do something based on what it reads in your game before you compile the exe. Once you've made an exe, you're not changing it, and Blitz3D is a compiled language, not interpreted, so nothing in any .BB source file is going to be understood automatically at that stage.
Config files are just text files. You read them with ReadLine and ReadFile and you write them with WriteLine and WriteFile. What effect they have on the program is entirely up to you, which is to say you have to write the code to read them and do something based on what it reads in your game before you compile the exe. Once you've made an exe, you're not changing it, and Blitz3D is a compiled language, not interpreted, so nothing in any .BB source file is going to be understood automatically at that stage.