The IN is as clear as it can be.
Candidates who have already commenced an examination series (sat one or more examinations) under the old syllabus, but have not completed all the required examinations for Licence issue before 1 September 2013, will have to complete any outstanding examinations to the new syllabus standard.
From 1 September, the candidate will continue with the new exams. The above mentioned exception is FPP&P and Nav, where you need to pass both for them to count.
Fighting an examiner on this, however, can be hard. I once had an examiner deny one of my students use of a calculator (simple one, no aviation functions, non-programmable) in the Nav exam, against the official CAA guidance which permits them, and he continues to do so. I now prepare my candidates for that, as he is the theory examiner of the school.