Hi Goagain. There was a thread by someone who ran in to the same issue as you a few weeks ago. Bear in mind I tend to do exUK or exEU travel so I think part of this was me not having any experience of booking two longhauls and trying to UuA just one sector. Here is the link.

http://www.flyertalk.com/forum/briti...-yq-twice.html

So that poster had booked US(somewhere)-LHR-DEL all in WT+ and wanted to UuA one of the longhaul sectors. After some digging it became clear he/she was being quoted an additional YQ for both sectors rather than just the one they wanted to UuA. Anonba who works for BA and is familiar with the system they use noted exactly the same as you have, which is tha the system show an additional YQ for CW for both legs rather than then only the one. Unless you realise it isn't right it and challenge it, it would be unlikely the agent would notice. I think the result was that the poster did manage to get an agent who could manually calculate the correct amount of additional YQ just for the leg which would be UuA'ed, but it wasn't easy.

As you noted, for exUK trips this is never an issue as when booking WT+ or CW, there is no upgrade as such of the domestic legs and there is no additional YQ to pay for those. For exEU trips I think if it is doing it the difference is marginal. I know when you book connetion flight YQ isn't really just the YQ for seach sector added together. However, to give you an idea YQ in Y AMS-LHR is €28 whereas YQ in J for the same flight would be €32. So if you have AMS-LHR-JFK and do UuA the longhaul from WT+ to CW, and BA's system is calculating additional YQ for both flights, realistically the additional YQ for the shorthaul is going to be pretty marginal.

So, it does seem there is an issue for doing a UuA for one leg from WT+ to CW when you have a longhaul connecting to a longhaul, but it does seem that it is possible to get the right price eventually if you persist and explain the issue to the agent. Note that this would not be an issue when doing a UuA from Y (so Y,B,H) to WT+ or CW to F since in both cases there is no additional YQ to pay for that UuA.