That is simply what we call the change in 'Magnetic Variation'. I suspect nothing has actually changed.
That's possible. But there are also some questions rised about the distance of both beacons from the runway threshold, and a small change of the runway threshold elevation. Those are maybe small details, but still worth asking, as there are too many of them.
1) They were probably set up for an autopilot 2-NDB approach, 3 degree glidepath, with the MDH set on the Radalt because the autopilot won't take Baro Alt inputs?
I finally found some time to start reading ABSU-154-2 autopilot technical manual. Original text in Russian. Well over 1000 pages.
On the first pages there is a list of functions of the system. One of them is barometric altitude stabilisation. Nothing about any radio height stabilisation.
4) At the last gasp they forgot they were on radalt not baro alt, or they didn't know about the ravine?
Just my guess. They were using radalt according to the FM, but didn't knew about the ravine.
Arrakis