the pump discharge must still be at a much higher pressure to overcome the burner (air) pressure
Seems like a great spot for a backflow check valve, wot? Of course absence of fuel flow for any duration will tend to cause flameout also, but a pulsing flow mode might be the natural result in a fuel choking-foaming situation if some type of check valve is present inline at the outlet side of the pumps. Isn't it likely the igniters were full on at that late stage in the descent?
Even if the foamy froth I described were re-compressed to a higher pressure, the new fluid likely would still have a notably lower density and some different physical properties due to the disruption of the original fuel fluid structure and consequent rejiggering of the intramolecular van der Waal's forces in the resulting froth. The aereated fuel would almost certainly have a lower density than the original JPxx for
any given flow pressure.
The phenomenon is rather like those products one purchases at the store which once removed will never again fit into the original box.