Just this morning I had CP do a change to my boarding pass which originally was issued with my Cdn+Gold number. Decided I wanted to use the flight between YEG and YYZ for my AAdvantage Gold Challenge (since it is year end and any more Cdn+ miles won't make much difference to my elite level status). Agent in Empress Club had no trouble changing the number over and issuing me with a new boarding pass bearing the AA number. Did this a few months ago in YVR as well, using that segment as the first for AAdvantage and the 100K promo, and it posted to AA within days.

As for IB, I flew BCN-PMI for a day trip and had the outbound credited to Cdn+ and the return to AAdvantage. There was no problem changing my Cdn+ number from the earlier flight on the PNR to my AAdvantage number and the AA one posted within days! (The CP was a slight problem in that I noticed when I got home that the agent had left out a digit, so I have mailed the boarding pass and ticket copy off the Vancouver for posting.)

Since I always check in at the J-Class counters, generally staffed by senior agents, they seem to be able to make these changes of FF program without problem.

My problem has arisen with AA's inability to handle their IB codeshares as AA flights, and recognizing non-accrual fares as being eligible for the 100K bonus. But that's another story...