Japan suffered a 9.0 earthquake in March and its high speed rail system is still there; it took about a couple of months to fix up the Tohoku high speed rail line. (More ordinary trains and railways have a bigger problem, as a tsunami swept away the slower trains' tracks).
Furthermore, CaHSR will not be swallowed up by San Andreas. It might get broken along the line of the fault wherever it crosses the fault, though, but San Andreas is a strike-slip fault, basically meaning that one side of the fault will move to the left and the other side to the right.
http://www.yomiuri.co.jp/dy/editorial/T110430002784.htmActual effect of 9.0 earthquake on HSR system.
