Thanks for the answer.
I am using Matlab to build the model and the S32 Design Studio for ARM to download it to the EVB.
I tried what you suggested and did use the "Download Code after Build" functionality. But the issue is not yet solved.
I had a Programm running that was generating a PWM on said pin and then build the model. Afterwich the pwm was off, what makes me believe, that the code reached the board but is faulty in a way or another.
I also double checked with a diffrent model. That one reached the board just fine (with both procedures, as you described and using s32 Design Studio)