The AAIB reports states clearly that there was no fuel contamination or water present in the fuel from the main tanks. This however does not exclude waxing, since it was likely to be gone at the time the examination started at a ground temp of + 10°C.
The cold soak this a/c went through was extreme and prolonged. Pilots on the earlier thread said they descended to lower FL. On the BA38 flight, TAT dropped to -45° and fuel temp -35°. But that is, fuel temp as senses by he fuel temp probe in one of the main tanks. It seems possible that somewhere down the fuel path, the actual fuel temp might have dropped further, as there it would not be protected by the inertia of the large volumes in the tanks. Pressure drops caused by suction at pump inlets would have made the temp drop even further. (Temp directly proportionate to pressure)
All of this could have caused local waxing and restriction, until an equilibrium was created during the cruise between fuel flow and temp drop somewhere along the path. at TOD, the thrust decreased and so did the flow, thereby increasing the restriction until a new equilibrium was created.
When more thrust was demanded, this was at first supplied to a certain extent thanks to the fuel volume in the lines between the restriction and the throttle valves, this creating a vacuum in the rest of the line, with possibly a very turbulent flow or even a shock wave and cavitation as a consequence. As the restriction prevented a higher flow than the one created by the last thrust reduction, thrust went back to that equilibrium, somewhat above flight idle. The time differential between engine 1 and 2 returning to idle could be explained by the difference in distance between the restriction and the valves.
Once on the ground, temp there would rapidly make the fuel in the restriction return to its non waxed state, leaving no trace? or would it leave a trace in the composition of the fuel??
It seems to me that serious thought should be given to prolonged 777 operations in very cold temperatures and the effects it has on the fuel temp along its path.