It happened to me some years ago.
Upgraded a CW to F ex BAH (20,000 miles) and never saw the miles come off the account.
HOWEVER, some months later I was due a 20,000 mile compensation for no IFE in F ex SFO (filled in card given by crew) but the miles never got posted.
So in this case it evened itself out, and I didn't have the heart to bang the drum about my missing miles.