So if I understand it correctly, they took off in Khania with 17t of fuel, couldn't retract the gear but continued anyway, the FMS showed not enough fuel to reach Hannover so they replanned Munich which was ok with a reserve of 3t, the FMS knew about the increased fuel flow but mislead the crew about remaining fuel at destination? Strange system!
What would have happened is that on re-planning MUC it might well show 3T. That figure would then reduce as the fuel was burnt above expected. As I said, the back of a gas bill envelope would have shown them they would run out
The ONLY strange thing here is when we do not want to understand the system.
Ofcourse it might have showed CORRECTLY 3 tons or whatever at early stage of flight, BUT for that part of the flight WIND dir/speed.
that must have changed after passing Zagreb. Especially if the crew did not enter every stage of the flight wind dir/speed, in the FMS, given the situation.