In general I think it calls save_settings(), which is in includes/adminfunctions_options.php. If you were writing your own code to change the setting, you could just update the value in the settings table in the db, then call build_options(). If you want to do it in response to one of your mod options begin changed, then you need a plugin, maybe on one of the hooks in that function, I'm not sure.
I'd figure it out, but like I mentioned I believe Ozzy was just talking about something like this so I think he'll know off the top of his head.
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