Have the same issue at the moment (my flight is paid by my Company with a different return from Mme FR).

Called AF - they can't "merge" the bookings, but they did offer o send a fax o the "service disinction" (...) in order to do a "Rapprochement Familiale" in order the we would be sure to sit together in the front of Economy - although that's not enough to get us both upstairs on a 744 for free...