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No, it shouldn't affect operation of stock lights. The way the kit works is that it takes both incoming signals and applies power to the indicator. The reason the stock wiring causes the 4 LED blinkers to flash at the same time is because the circuit is in a loop and there's no terminating ground at the indicator. The bike relies on the turn signals and indicator to draw enough power to keep the opposite side from blinking. This creates a ground at the indicator so that power isn't fed back thru.
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