I've never tried anything like it, but you could attempt to edit them for use while it is running, then when you quit mIRC, use an on QUIT event to write them again. I don't know if that will work, or not. It's worth a try.
Alternatively, you could change the setting while running mIRC and save the settings as a variable, then have the script automatically change them to what the variable is set to on START.
