The linear PM BLDC motor(LPMBLDCM) used in an electromagnetic launcher has a short broken permanent magnet(PM) mover whose end magnetic field is deformed. When hall cells are used in detecting magnetic induction and helping realize phase change, the phase change points(PCPs) will be shifted by this type of end effect. The phase change principle of the LPMBLDCM was analyzed and how the short broken PM mover shifts the PCPs was presented. It was concluded that this type of end effect is mainly affected by the pole-arc factor of the PM poles. An asymmetric hysteresis comparator, as well as a common single threshold comparator, was used to reshape the output of hall cells to eliminate the influence caused by the end effect. Experiment results of a prototype motor prove that the common single threshold comparator method is feasible.