Please bare with me, my knowledge and experience with miproms are limited.
John Jay brings up a valid point. Not knowing which drive is being utilized leaves us incomplete.
Now this is where I'm unsure of myself. It's been sometime since I've worked on this type of equipment. But I thought that if both SF & HF LEDs stayed on it indicated a problem with the drive.
I am woundering, you said the encoder coupling broke? Did you replace the encoder? Is it possible that the encoder is causing a fluctuation in the velocity demand that in turn creates an HF emergency stop?
Also could it be the drive I/O board or relay pilot board?