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Can you give a bit more detail about your system, and what problem you are trying to solve, and how this will achieve that?
By "planner" I assume you mean the trajectory planner?

I am now even more confused about what's going on.
Are you actually hitting the limit switch? Or do you mean that you jog to the top soft-limit, zero the coordinate system, and then jog away again this inexplicable offset appears?

Do you have anything like external offsets enabled? Any unusual kinematics?

if you want to try i added dedicated hal pin to the spindle encoder index, you can connect it to any input pin, and you can define in the config.h and also set the active level of the signal to active low or active high.

If the original manufacturer thought that is was important enough not to require homing to go to the trouble of fitting potentimeters I would be inclined to follow their lead.
I don't think it's a difficult thing to integrate.

I see you have two slaves with idx="0", that won't work.
List the indexes with "ethercat slaves"

There is another debug option or possibility. The output of "sudo dmesg" show a lot, at the end it may have info that can show the error.
Especially info messages from ethercat master and lcec goes there.

Good morning, I want to update my Qtplasma and would like to know if there is a step-by-step guide for doing so. Thank you.