A little late for the OP, but whenever you get a flight switched from one carrier to another that is a member of another alliance make sure you ask the original agent to grant you original route credit.

When you get to the other carrier's counter, have them plug your FF number for that alliance into the new flight.

On an award travel and they change your flight/routing? Make sure they enter your FF number on the new segment. I have always earned miles by doing just that.