'What do you do ____ your job?,'(A.in B.at)
Rachel: 'in' seems to refer the activity in any job, but 'at' seems to refer to the place where a job is performed.
For example, we might ask Jill, whom we have just met: 'Oh, so you are an environmental city planner. What do you do in that / the / your job?'
We might ask Jack, who works in the technical department of our company, 'What happens to our computers when you take them away? What do you do at your job down there in that room where all the broken computers are?'
Okaasan: In your job seems to be asking about the technical aspects, or perhaps what a person with that job title does. "Well, what IS an environmental city planner? What do you do in your work/job?"
At your job seems to be asking about the details of the person's work, or (as in Rachel's example) perhaps implying that the person isn't getting any work done. "What do you DO all day at your job/work? Why isn't my computer fixed yet?"