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I tried a bunch of stuff, this are the results:

1. I tried to set the corresponding PDO assignments via EtherCAT-Configurator once again. It changed the PDO assignment but after a power-cycle the settings were gone.

2. I tried to set the PDO assignment via a InitCMD-XML file. The InitCMDs do not change anything unfortunately. A "ethercat rescan" didn't help either, it just caused more errors in dmesg (output attached)

3. Your linked your software "convertorSdos.exe", i wasn't able to use it properly, it errored out with a "Unhandled exception. System.NullReferenceException: Object reference not set to an instance of an object. at Program.Main()" and crashed entirely. I started it with the "Beckhoff_EP5101-0011_config.xml" in the same folder, typed in "c -i" and gave it the absolute path to the before mentioned XML file - what did i do wrong?

Thanks for answering. When i run this code from examples its do. G21 G54 G18
F400

O100 SUB
G0 X10 Z0
O101 REPEAT [3]
G1 X[#<_x>-5] Z[#<_Z>+3]
G1 X[#<_x>-5]

O101 ENDREPEAT
O100 ENDSUB

O101 SUB
G72 Q100 X1 Z1 D0.5 I1 R0.3
G70 Q100 X1 Z1 D0.5 P3
O101 ENDSUB

O101 CALL

M2
When from this code i delete G72 line G70 working fine . But when i change G72 to G71 Linuxcnc freezing . Can someone direct me to right path. How to run G71 .
.

if you: 

1. Disconnect the encoder

2. Change the index input to TTL mode
(W1 left)

3. With LinuxCNC running and halshows "Watch" tab showing
    hm2_7i96s.0.encoder.00.input-index, does the state of
    hm2_7i96s.0.encoder.00.input-index change when you ground
    the IDX+ input (TB2 pin 13)?

My wiring is good. I followed the MESA7i96s documentation. I think everything is correct.
I've tested 5 RS-422 encoders with phase A+,A-,B+,B-,Z+,Z-. Or maybe my MESA board isn't working properly. I don't know how to get out of it

Good point I forgot to mention the specs
Current is 3A. Resistance is 1.3 Ohm
Holding torque 3 Nm
I run them with a 36v power supply.

O guess that about no voltage specification is a good point you don’t know what transistors are in there.