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I have see value 1 on much example the xml file and not have problem with this value on debian 10 , lcnc 2.9.0-pre0 and ethercat 1.5.2.

I have test on debian 12, lcnc 2.10.0 and etehrcat 1.6.3 with value 1 and 5 and 1000 , but have error synch 5000 ms foe every drive.

only with -1 the error disappears.

What I don't understand is why on Debian 12, when LCNC starts, the PDO information is written to HAL after a few seconds and in sequence, one Ethercat node at a time from 0 to 5, while with the Debian 10 configuration, the PDOs are immediately read and updated in HAL, as soon as LCNC is running.

another difference between debian 10 and debian 12.
I use PCs with two ethernet ports.
With devian 10, with ip a I have 2 network cards enp1s0 and enp2s0,
while with debian 12 I have three, the two physical network cards and one with written: eoe0s0, which is created when ethercat is running.

Could it be that ethercat 1.6.3 unlike 1.5.2 uses a virtual card that in turn closes on a real one?

Why do you use refclocksynccycles=1? That's low.

for 2.5D you can try github.com/multigcs/viaconstructor/

As for as I know Heidenhain LS403 is a 11uA signal . Not 1Vpp.
Please check the datasheet