All of CO's evidence will show that you were in the FC seat.
Twice in the last year, I saw my upgrade after I had already taken my Y seat. In both cases, I went ahead and took my seat, and (after sitting down) said to the FA, "when the GA comes on board with my new BP, please let him/her know that I've already taken my assigned seat." In one case, the GA appeared a moment later with the BP. In the other case, I saw the FA say something to the GA, who left the plane, then returned with the BP. Not sure, though, if I would not have gotten the upgrade on that second flight.
My view - 1) if it's on your PDA, then it will be on the manifest. 2) if calling you up for your upgrade is a pain for the GA and FA, it will be an even bigger pain for them to downgrade you when you're holding the evidence in your hand.