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I think I know what's wrong. The microcontroller is doing throttle proportional to current. So, let's say you give it 50% of full throttle. It will ramp up the pwm duty until the current sensor feedback is 50% of 500 amps. But with LEDs that's never going to happen (250 amps), so what you get is ramping all the way to 100% duty but with essentially zero current feedback, which is a fault, (since 100% duty and no current won't ever happen with a real motor), so the yellow led blinks fast.
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