Setting up the Stepperonline A6 battery encoder cable

Regarding the post above:
Yes, you're right,
CIA homing isn't really well documented yet.

In principle, it works like this:
The CIA-home function triggers the servos' internal homing routine and monitors the status. Once the servos report completion, CIA-home signals to LinuxCNC that homing is finished.

The drive error after homing is normal.
This happens when CIA-home hands control back to LinuxCNC.
Make sure the lowest feed rate is set; the axes will then synchronize without errors.

Yes, it seems to be the case. I seem to have better luck when deleting position file prior to opening linuxCNC and homing, it works without issue most of the times. The issue i had with the Z motor turned out to be a slight misunderstanding of the process on my side, i still don't have a z axis and I was simulating the homing switch hits triggering the sensor manually, but turns out the process needs the sensor to become hit again on the second pass before it'll attempt to look for the z pulse.

@andrax are you on an XYYZ machine like your posted config suggests? can you respond regarding how the Ys sync up with the absolute encoder? The other thing i'm concerned about is if I should use homing mode 20 instead of 4 for Y, because otherwise the z pulse step becomes something that'll mess up your parallelism without you being able to adjust by adjusting the sensor triggers

Why make it so complicated?

Just use CN1.
Simply connect the home switch DI3 and COM pin 13 here. Use the wiring diagram on page 47 for the external power supply.
Use homing mode 4 or 6, depending on where your home switch is located.
If everything works and you have encoder cables with batteries, you can switch everything over to multiturn absolute encoders—which don’t require homing—by following the instructions above.

I wrote these instructions because there are issues with XYYZ (gantry) axes. 
Explanation:
During CIA402 homing, control and monitoring of the axes are taken away from LinuxCNC. The internal servo homing is triggered. You can only see the current position of the axes and how they are moving. Once the axes have found their home position and report that they are ready, control is returned to LinuxCNC. This results in several problems that can become dangerous!
1. After homing is complete, the axes may jump, leading to an error. This has already happened to you.

2. With gantry axes, there are synchronization issues. It can happen that one axis starts moving late or not at all. In the worst case, the gantry will be crooked or break.

3. Once homing has started, it cannot be interrupted.
Neither an emergency stop, a reset, nor disabling the enable signal will help. The servos will start moving on their own once they’re enabled again. The only solution is to turn the servos off and then back on!

Using LinuxCNC homing isn’t an option either.
The Z-index pulse isn’t output by the servos and isn’t available. Of course, you can also use LinuxCNC homing by moving to the home switch or limit switch the traditional way, but that’s imprecise and suitable only for a cheese cutter at best.

That’s why I wrote this guide.
Here are the steps again:
1. Get everything up and running. If you run into problems, there are many threads here that can help, or you can start a new thread.
2. Get CIA homing to work with the servos removed.
3. Convert the servos to multiturn absolute encoders following my instructions.
4. Install the servos and, on the gantry, make sure they don’t twist—otherwise your gantry will be crooked.