Comment by mikkupikku

They made the right call, kind of, and only by accident. John Young had telemetry for the flap available to him in the cockpit but didn't notice it happen at the time. NASA ground control also had the telemetry, but also didn't notice / understand until after it was too late to eject (which was only possible during a narrow window for ascent, and not at all for reentry if the body flap had been inoperable.) They also simply got lucky the hydraulic system performed beyond it's designed safety margin.