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I have actually accidently done this when I first got my macbook and set both the right command and right option as an option key. I don't remember how as when I exit both SEIL and Karabiner it still happens.

Does anyone know another way to do this without karabiner and seil? I am using El Capitan.

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After watching the response in Karabiner Event Viewer I reset a couple times the defaults for the external keyboard in the modifier keys. Resetting command and alt a couple times seemed to make it work properly again. I guess because I had switched them before and maybe the keyboard wasn't recognized properly. All is fine now.

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