To mook, the situation you described sounds like a problem with the HEP, either at the Locomotive or with the cables to your car. Although Amtrak Engineers have been known to drop the HEP supply to the train to boost the horsepower available for traction, I doubt this would apply to a San Joaquin. This occurs most often when climbing grades with less than the desired number of units available, or with problems getting the engine to load properly. This tactic was quite common on Train # 36, The Desert Wind, when climbing Cajon Pass with only 1 F - 40 for 7 cars.
The first clue that something was wrong on my Leavenworth Snow Train was when all onboard lights & AC shut off, leaving us in the dark in a 8 mile long tunnel. The train continued on for a ways before the locomotives shut down completely. Lotsa fun up in the dome.