Leg of code share booking showing up twice in bookings of operating airline
 

Hi,

I've made a booking for IST-LHR-BOS / BOS-LHR-HAM via American. The operator of all four legs is BA. I've got one booking reference from American, which has been split into two bookings with BA (where I can see them in my EC account). So far, so good. The problem now is that the leg LHR-BOS shows up on both of the BA bookings. I.e. the BA bookings are for IST-LHR + LHR-BOS, and for LHR-BOS + BOS-LHR + LHR-HAM. To make things even more complicated, this one duplicated leg shows up with an Iberia flight number in the AA booking.

Is this going to be a problem? I am concerned about getting the return flight legs on the second booking canceled for having a no show for that first leg. Of course I am planning to fly that leg, but I could only choose a seat for it from that first booking. Maybe things will clarify when I get the boarding passes, I don't know? I called BA about it who told me that it may be a problem and I should call AA to get it sorted out. Which I did, and they told me, it's fine. Has anyone encountered something like this? Thanks a lot for any advice.