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Sorry for the late reply, when I plug it in I just get a single solid light for a second. Is there a lock of some kind? Sorry if I missed this info somewhere.
That means it's in HAS mode which disables remapping. It's a special mode designed to eliminate conflicts with the HAS supergun's built in remapping capabilities. To disable HAS mode you need to hold L + R + Start for 5 seconds. It you will then be back in standard mode and button mapping will be available.