I might suggest you not worry about "feeling bad" about doing what your job requires you to do. If it is part of your job, that is just what it is and try not to get into questioning everything your employer asks you to do as part of their office procedure. You are not the patient here nor the practitioner. You are simply the employee. This is something to be cognizant of in this new job where you are dealing with things/people you feeling personally involved with because of the relation to your therapist and your own therapy experience. You are going to have to keep a disconnect there or that could potentially become a problem for you.