On my usual itinerary, there's been no problem, either before or since the change. Check in at BOS for QR 744 and 668, BOS-DOH-CMB. Show them my separate UL itin (booked completely separately on UL's website) CMB-BKK and they're happy to book my bags all the way through, BOS-DOH-CMB-BKK and issue all the boarding passes. Easy peazy!