I got a bridgeport-style vertical knee mill a few months ago with an Anilam 3000 CNC system.

Everything seems to work, except the Y axis is inverted. I really need to get that fixed.

The software has a phase invert option in the axis setup pages (which a manual says is the only software way to invert an axis), but enabling that will cause the axis to jump in one direction when the servos come on for a second until the controller detects a fault and shuts it down.

Is the problem that the encoder needs to be inverted as well? I can't find a software way to do anything else. So, I'm looking into hardware wiring changes.

Each servo amp has four thick wires (orange and gray appear to be servo amp power, violet and blue go to the servo motor) and five thin wires on a long white connector (two black, two red, one blue). Which wire should I swap? I figure I need to swap both servo and encoder wires. (?)

I set up one axis to move back and forth at feed rates, and measured +6V across the violet and blue wires in one direction, and -6V in the other. I tried swapping these wires, but then the axis just took off very quickly on servo power up and after hitting the e-stop I was 0.5" from crashing it! I figure I also need to swap some encoder wires. But which?

The wiring appears VERY similar to this 3000 setup on another mill: https://www.pts-tools.com/MSDS/RL60MB10R.pdf (page 57 of 77)