Analise,
I have managed to get an extra segment credited to my account for a flight that was cancelled at the last minute by CO that I never flew (EFD-IAH) the short puddle jumpers within Houston, but I have never tried to skip a large portion of my iterinary.
I believe that CO processes segment and mileage credits based on boarding passes that the gate agents collect. If your pass isn't among those that the agent collects then you normally won't receive credit for that flight.
If anyone else knows a way around this, I'd sure like to hear it.