Hmmm... I dunno. From Dancing Lessons:

Watch me pull a rabbit out of this hat.

Hey wait. No rabbit. Where'd it go?

It would appear that if you make any change to your itinerary -- different flights, different dates, different seats, whatever -- you points for that segment will not be posted. Doesn't matter how small the change. Doesn't matter how many times you ask different people to re-insert your FF number on the PNR. Doesn't matter if they engrave your FF number down the entire length of the plane in 3 foot high digits -- it ain't gonna happen. Keep your boarding passes.