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Alternative, you might be interested in the auto configure functionality of RetroArch: essentially, it changes the input settings depending on the controllers that are currently plugged in and supports hotplugging. You can find more information about that at (quite at the bottom that site)

I never found time to have a deeper look into that, but I think that it might even be worth to be included into the RetroPie Script. Any help here would be greatly appreciated!