We use the two target repeating earthquake sequences of SAFOD to identify time varying properties of the shallow crust in the Parkfield area at the surface and in shallow boreholes. At the surface, we find that the 2004 Parkfield earthquake caused direct S wave delays exceeding 7 ms, and S coda delays exceeding 15 ms. We attribute these delays to cracks formed or opened during the strong shaking of the Parkfield earthquake. Observations at depth show that the direct S wave arrival time was much less affected by the Parkfield earthquake. This provides evidence that damage caused by strong shaking (nonlinear strong ground motion), is limited to the very near surface (<100 m).