This sounds familiar. I was booked on a full fare Y with CX from KUL to HKG in August. I arrived at the gate, to be told that the flight was overbooked. They asked if I could take a later flight - the deal was that I would be upgraded to J, and given a hotel for the 4 hour wait. As I was not in a hurry this was OK.
For my later flight I was given a J class BP with a CX flight number, but the flight was operated by Malaysian. The miles didn't post. I chased this up repeatedly, but was told by both BA and CX that my ticket was not traceable. Eventually I admitted defeat.
I remain somewhat miffed about this. My booking was with CX on a tier point eligible flight. I accepted being bumped without compensation. I flew on a CX flight number, but still got nothing. Not impressed.