I ran into this same issue but I had already completed the exotic sword. What I did was I put all my swords (including the exotic) in the vault. I grabbed one of the swords on the one character I used to upgrade and got the 2nd exotic quest on my Hunter. This morning the 3rd showed up. The quest is designed for only one per character. So the system still sees that you have a quest unfinished. You can do two things you can finish the quest and the put all your swords in the vault. Then take a legendary sword that you don't have the quest for on the character you used to upgrade. Or you can put them in the vault and grab it now without doing the quest first I'd suggest doing the exotic quest first