The way I flush a heater is...leave the cold supply on, open the bottom drain valve and drain to a floor drain, utility sink, bucket, etc., until it runs clear, close drain valve. Then open a hot tap on a utility sink and run water until that runs clear, turn the heat back on. You should now have all 'stuff' flushed from the tank.
That process blasts the bottom of the tank(where the worst of the stuff has accumulated), and flushs it out the bottom drain. There will be some of it that gets stirred up and needs to be flushed out, second step.