Simple:
You sit the exam.
You fail: the examiner sends a form to the CAA, who keep it on record.
You pass: usually, the examiner at the school keeps it in his files (not the school's, it is confidential) and then the school gets him to fill in the bits on the licence application form and sign them at the end of your training.
If you just do some exams with an examiner, ask him/her to fill out and sign the relevant page of the licence application form there and then. Them when you sit the other exams with a different examiner, ask them to fill out the remaining subjects on that original form.
Of course, if you have failed an exam - and go to a different examiner - tell them which exam set you failed (ie Nav M02). Because you would have to sit Nav 01 or Nav 03 so as not to sit the same exam twice! (exam numbers made up)
If you were to sit Nav M02 twice, when you apply for your licence the CAA would see from their "failed" file that you set the same paper twice. So your license application would get refused.
I hope that makes sense. But any examiner should also be able to explain.