Symptom: On power up the machine would not home in X. It would go until it hit the X limit. Here is an abbreviated log of what fixed it.
We verified the encoders were present at the encoder with an oscilloscope. We made a short cable so that the stock cable coming from the encoder could be made to reach the back of the Heidenhain without using the long cable. The extension cable was cat6 network cable, 4 pair and a shield for just enough connections. The machine worked so we decided it must be the 5 meter cable routed through the machine and removed it. We checked it carefully for continuity and shorts and found none. Then we put the 5 meter cable which was then out of the machine in the path with the short extension cable and the machine homed. But when we took the extension cable out the path the machine would not home. So there was something going on between the green connector inside the encoder cover and the pins it mated to. The extension cable we made had new parts for the male end and the female end. So our fix was to make an extension cable very short so that it would fit inside the encoder cover. That seemed easier than trying to put new ends on the existing cable and circuit board. We had tried a second stock encoder cover with a cable attached and that did not fix the problem. I can't imagine how the square pins on the circuit board were the problem. But the machine has been running for several hours and several cold starts without the problem coming back.

As I understand the problem, the encoder signal that occurs once per revolution was not being seen by the Heidenhain control.

Error messages:
Measurement system defective A
Extreme Axis Limit