Combining folios has resulted in either one room posting correctly, or one room as zero points (the one that the hotel combined out of leaving an 'empty shell' as it were).

Keep your bills (folios)! Odds are you'll need to submit both showing your name and number on each. One quirk I have hit was that Hilton CSRs have refused the 50% Diamond bonus on both citing, 'You're only entitled to that for the room you, the Diamond member, occipied.'