If you had cleared the extra time thing with the examination officer beforehand and they said that was fine, and then didn't give you it - then you should speak up. But yeah, I don't think the GP's word is final, your school has to have said yeah that's ok to it also.
With regards what happens when you don't go in for the other exam, nothing happens. It will come up in your results in August 'U' and you don't have to declare it to your universities. I did the same thing last year.