a lot of people get confused here.
flipping the polarity inverts the waveform - phase is to do with a slight time difference of the same wave when picked up by different sources.
if something is exactly 180 degrees out of phase with something, then hitting the polarity switch will fix it - otherwise to get things perfectly phase alligned AFTER its been tracked you'd have to nudge the waveforms very slightly.
if its almost 180 degrees out and you hit the polarity switch you may be minimizing the phase effects but certainly not resolving it entirely.