We have used a separated beam atom interferometer to investigate magnetically-induced phase shifts of the different magnetic substates of the sodium ground state. We have observed periodic rephasing of the 8 independent magnetic substates present in an unpolarized sodium beam as the differential magnetic field is increased on opposite sides of the interferometer. We have also demonstrated that two phase shifts with similar velocity dependences can be used to cancel each other, creating an interference pattern from one magnetic substate although an unpolarized beam is sent into the interferometer. Finally we discuss some applications of these techniques.