Just an update:
i didn't realize that i had to change also the transformation execution from local to the carte remote server for my transformations that lives inside that job.
Now the file not found error is disappeared, but the transformation now seems to not even start.
From the job and transformation status view in Spoon i see that the transformation does not even execute and the job ends with no error. The only log i see in the transformation is this entry: "Dispatching started for transformation"
But then nothing else.