I hope you don't take the words change to mean remove and replace.. it just means to switch the connections coming from the speed controller to the motor. Example if your wires were red blue and white with red matching up to red blue to blue and white matching up to white all you would need to do is simply switch any two of them and leave one un changed so say you left the white to white then you would have red going to blue from the speed controller and blue to red again from the speed controller...

if you switched polarity from the battery to the speed controller you will burn the speed controller so if you did something like that then that could be the reason it no longer works. I hope this helps.