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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.

You`re right. When I realized that it is a special customized Version I started everything all over again to go with the simplest version. I did what you proposed and compiled the cia402_homecomp. Than I mixed my working Beckhoff starting point files with the ones from dbraun. Unfortunately it still crashes:

wopass: load_the_modules cmd=<orig_loadrt lcec>
waitpid failed /usr/bin/rtapi_app lcec
/usr/bin/rtapi_app exited without becoming ready
insmod for lcec failed, returned -1

Shutting down and cleaning up LinuxCNC...
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments

Debug file information:
Note: Using POSIX realtime
motion.c: Creating unlock hal pins for joint 4
LinuxCNC Ethercat crashed with signal 11
-- STACK TRACE START
0 /usr/lib/linuxcnc/modules/lcec.so(+0xfc8c) [0x7fc1af3e9c8c]
1 /lib/x86_64-linux-gnu/libc.so.6(+0x3c050) [0x7fc1b0303050]
2 /lib/x86_64-linux-gnu/libethercat.so.1(ecrt_slave_config_pdos+0x2f) [0x7fc1af3ad52f]
3 /usr/lib/linuxcnc/modules/lcec.so(rtapi_app_main+0x40a) [0x7fc1af3eaf38]
4 /usr/bin/rtapi_app(+0x10cd7) [0x56167d468cd7]
5 /usr/bin/rtapi_app(+0x1162e) [0x56167d46962e]
6 /usr/bin/rtapi_app(+0x11c2c) [0x56167d469c2c]
7 /usr/bin/rtapi_app(+0xc974) [0x56167d464974]
8 /usr/bin/rtapi_app(main+0x70f) [0x56167d46444f]
9 /lib/x86_64-linux-gnu/libc.so.6(+0x2724a) [0x7fc1b02ee24a]
10 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85) [0x7fc1b02ee305]
11 /usr/bin/rtapi_app(_start+0x21) [0x56167d464861]
-- STACK TRACE END
Waiting for component 'cia402' to become ready.....Waited 3 seconds for master. giving up.
.Note: Using POSIX realtime

2971
Stopping realtime threads
Unloading hal components
Note: Using POSIX realtime
lcec: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
motmod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
trivkins: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
homemod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
Note: Using POSIX realtime
tpmod: not loaded
<commandline>:0: exit value: 255
<commandline>:0: rmmod failed, returned -1
<commandline>:0: unloadrt failed
Note: Using POSIX realtime

Do you have any Idea what to try next?