My wife and I had a BF mileage ticket where the international segment didn't clear - the difference in points for her ticket (y to BF) didn't come back. MP PG phone agent couldn't help, referred us to customer service - web request led to redeposit of miles 2 weeks later.

I was on the same itinerary, also upgrading to BF, but using miles+copay on a paid ticket - mine came back - points after 1 week, cash after a further 2 weeks.