IW - you're right in that, until all of the test is done, you don't know if it's a pass, partial or fail. In this case it would seem that partial or fail are now the only 2 possible outcomes.
CY - your examiner has told you that part of the nav section has been failed. This means that the whole of Section 3 is failed. He can't be specific about what you'll have to refly until the rest of the test is done. If you are successful in the rest you will have to refly the departure, nav section and an arrival. If you fail any other item on the rest of the test then you will have gained a full fail and will need to be retested on everything.