"However, the main tank was not empty and both Xfer pumps have been tested by the AAIB, so if CAD had failed then surely as a matter of importance you would leave the Xfer pumps on?"
But then you'd be disregarding the drill in the RFM.....
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"The testing you saw did they run till indicated zero or flameout? Means the difference between a faulty low level device or a faulty probe system."
It wasn't a test, just a request from the engineers to run the supply tanks to minimum to allow them not to have to drain too much into a bucket before inspecting the tanks so it was a surprise to all that the warnings didn't come on and they may have been faulty for months or years prior to that.
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"If say 2 mins aftert the red came on one engine started showing symptoms of fuel starvation maybe the prime pumps were activated?"
Not sure about the symptoms, in my experience, once the flame goes out it's out, ie...instant.
IMHO I think the 4 pump switches were selected by simple mistake, but I have absolutely no proof, I've done it myself in the past but have picked up MY error on the CAD straight away.
As a simple test, stick a post-it note to the car headlining above your left shoulder with a drawn on diagram of 4 switches and labels, put on your reading specs and a baseball cap (after dark with the instrument lights on)and try to read it (driving at the same time would not be a good idea
).