Apologies if this has already been spoken about or dismissed - I haven't been able to read all 43 pages so far.
Some of the aspects of this accident just made me recall the following passage from and incident report (although RVSM/TCAS related) involving an A340 entering turbulence over the North Atlantic.
Feel free to disregard if irrelevant.
A340 commander's report
At FL 360 the A340 was 1000 feet below the maximum cruising level displayed on the Flight
Management and Guidance System (FMGS). The commander was expecting a turbulence
encounter around 59°N 20°W and when the aircraft first entered light turbulence he made a cabin
announcement and switched on the seat belt signs. Shortly before the AIRPROX event he
experienced moderate turbulence and noticed outside air temperature changes. Suddenly the aircraft
began to climb, the Master Warning sounded and the autopilot self-disengaged as the aircraft
exceeded the speed limit of 0.86 Mach. The indicated airspeed dropped below VLS (the lowest
selectable) as the aircraft climbed and the commander took manual control of the aircraft because
neither autopilot would engage. The crew subsequently reported the incident to Shanwick on HF
radio and using their TCAS, they descended back to FL 360 in a safe area. At the time of the
AIRPROX the commander estimated the aircraft were one mile apart laterally. After landing at
New York the commander had the aircraft inspected by technical staff but no defects were found.
There were no injuries on board the aircraft.
The commander could not remember the sequence of warnings but he did recall being unable to reengage
either autopilot which prompted him to make manual control inputs. He also remembered
seeing an 'Alpha Lock' warning displayed on his Primary Flying Display.