I have gotten miles in 2 programs, as mentioned, when a flight is cancelled, and the original airline books you on a different carrier. You should go to carrier number two, get a boarding pass that does not reflect your ff number with carrier 2, then after that give carrier 2 your ff number (with other agent or over phone etc), and then mail orig boarding pass (with no ff number) to carrier 1 that cancelled the flight to get credit on it as well.

I was also recently on a flight that stopped, but with no change of planes. Let say BOS-ORD-LAX. But one flight number. First was full bos-ord, but open ord-lax. So the agent rebooked the flights bos-ord in y and ord-lax in f. The agent wrote out something that looked like a fim for the ord-lax, and in bos they took the bos-lax original flight coupon. This way, I got miles and segment count for two flights, even though they were the same flight#. When I worked as a travel agent, I would book myself like this getting a separate segment/flight coupon for a continuation of the flight.......rather than booking it as a single thru flight. I don't know how willing most agents would be to doing this, but it never hurts to ask. The agent actually volunteered to do it, I didn't ask even.