It seems that:

- If there is an AA number in the system it takes that first - and on AA it's had to get them to change it so I try and keep all my AA segments into my AA account. If you replace your AA number on an AA flight NOTHING prints on the boarding pass for the FF number

- BA certainly can swop numbers - last promotion I had a nice lady do three segments with three seperate numbers all printed on the boarding passes correctly - we joked about her being the former BA MD's wife - yes and she still did it!