Are you using a SWU? If so, yes, you are supposed to keep your NC seats. However, during the process, the agent may forget to get your NC seats back because the computer does the refaring automatically and the agent must get the upgrades back. This has happened to me, but it was corrected. Now if you use miles to upgrade, I don't know the answer. If you upgraded an M fare and now it is cheaper, does it go to a V or Q which would preclude you from using miles? Don't know the answer to that.