Magnetic field trapped in the Gravity Probe B (GP-B) gyroscope rotors contributes to the scale factor of the science readout signal. This contribution is modulated by the rotor’s polhode motion. In orbit, polhode period was observed to change due to a small energy dissipation, which significantly complicates data analysis. We present precise values of spin phase, spin down rate, polhode phase and angle, and scale factor variations obtained from the data by Trapped Flux Mapping. This method finds the (unique) trapped field distribution and rotor motion by fitting a theoretical model to the harmonics of high (gyroscope spin) frequency signal. The results are crucial for accurately determining the gyroscope relativistic drift rate from the science signal.