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When signing in to a Nintendo Switch using Joy Cons, the screen will always show the color for them. But, how does it know? In terms of parts, all Joy-Cons seem just about interchangeable?

More importantly, can a user potentially change what color a Joy Con thinks it is?

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    It looks deep inside itself, then remembers the colour is on the outside, and looks there instead. – Paul D. Waite Jun 8 '20 at 14:45
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When the Joy Con connects to the Nintendo Switch via Bluetooth, it sends some data as a "handshake" between the console and the controller. In this data, the Joy Con itself reports the HEX Color and Side (L/R) of the controller.

This can be confirmed with a program called Joy-Con Toolkit that allows you to see and change the colors reported by the individual controllers just by connecting them via Bluetooth:

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