In my experience, I have got all miles for all flights I have taken, even though I have not travelled all sectors. Sometimes online retroclaim just does not work, send the BP by post and ask a few times during the next months, eventually you should get the miles. It can take a couple of months though, so I hope for you that they manage to credit the miles before the others expire. If not, you should get them back later, but it means more hassle.

Flights you have paid for, but not travelled, will not be credited.