I think you're going to have to keep track of some time marks yourself.
Chronometer myChrono;
long baseTime;
long stopTime;
long elapsedTime;
When you set the base time, you want to use:
baseTime = SystemClock.elapsedRealtime() - stopTime;
myChrono.setBase(baseTime);
When you want to see how much time has passed, use:
elapsedTime = SystemClock.elapsedRealtime() - myChrono.getBase();
Take a look at the SystemClock doc.