I switched the X and Y axes to their correct positions (switched drive terminal blocks) and checked that they moved in the right directions.
Next, I started troubleshooting my problem with the Z axis encoder signal. I found a few loose wires in their crimp terminals (the smallest I could buy were 0,25 mm2, and yet a lot of the wiring is still too small if some of the strands somehow got clipped; then I have to fold the wire in half and get it inside the connector again).
Anyway, now the machine won't stay latched on after the machine is on button is clicked

I was hoping to be tuning the servos today but I have no idea what caused this change. I checked all the relevant wires but after I release 3SH1, the 7RC2 relay switches off. It's not hardware estopped either since it turns on for as long as I hold the 3SH1 button. Looks like I just took an unnecessary step back