Clipper i've had a similar experience lately. In March i'm travelling JFK-AMS-PRG on KLM and KLM coded/CSA operated flight between AMS-PRG. Twice the CSA leg has been cancelled from my itinerary. Called NW (booked thru them) and they say that for some reason CSA is not getting the ticket numbers, resulting in the segment being cancelled.
Perhaps that's what happened to you too.