I have had this situation fixed many times and most agents are willing to do this for you. Recently an agent rebooked a HUP fare for me and it booked into Y (with A class available). I was confused (so was the agent) and he ended up moving the segements into F class.
UA agents have been generally very helpful for me when it comes to HUP fares and if things don't go your way you can always hang up and call again.