Good spot. Changed wires without unplugging the power… Now stepper does not move. Have to be away for few hours. Hope boards survived. Will try to flash on arrival. Poor me…
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few more hours of search. Stepper just went to move as expected.
The solution is to change the cable from Crossover to Straight connection to the stepper.
See the picture for reference.
Thank you team for the help!
I think this made it a lot more complicated, you should not need to change that, but as long as it works… 
Jus remember to write it down so you remember what you did when troubleshooting it some day.