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When the gauges started indicating a loss of 3 tons of fuel per hour, they probably started planning an emergency divert. SSGT Bachleda's observation would have sealed the deal.
It depends on the aircraft. Some FMS systems have sensed (weighed) fuel on board from each tank. Others expect a manual entry from the flight crew.
However, at present most aircraft determine their fuel usage through fuel burn via the fuel supplied to the engines. The rate is usually in PPH or pounds per hour.
Lately, and this is true on the new FMS I am helping to develop, there is an attempt to detect fuel leaks when the fuel cannot have been burned and the sensed fuel does not match the calculated amounts, the system would then alert the flight crew. It's not easy to do, but I think it is worth it especially on larger aircraft where more lives will be saved with such a system. The reason it is not easy to do, is largely because it becomes complicated to determine where the leak is occurring, before the fuel pump, or at the fuel pump. It requires the FMS developer to have access to a lot of information from the airframer, the engine/FADEC manufacturer, and the fuel pump manufacturer as well.
Presently, in deployed FMS fuel management systems, this capability doesn't exist. But if a fuel leak does occur, I suspect the auto-flight system would start trimming the control surfaces as far as it could compensate and then decouple if the FMS could not automatically reroute fuel to balance the aircraft. It really depends on the specifics of the listed aircraft systems and EICAS alerting in this instance.