I've played 2 and won 2 but now can't find another player for my 3rd encounter. I read that the new update allows for better syncing but there aren't always going to be players so after waiting say 5 minutes you should play against an Ai for a chance for the reward or be given the reward automatically.

Where can i go to retrieve my duel for my reward? Is it in the barracks? I had to cancel because no one synced and now it's gone.

After winning you normally get the reward automatically and the Arena will disappear. But sometimes it does not registrate your win so you can play again. It seems it does not give the reward when you don't keep waiting and go back to the warzone idle or to your dashboard or to just any other place. But if you can open a new tab to do something else while waiting for a match, it will registrate your win.

Considering you are saying 3rd encounter i'm guessing the template is the four castles FFA Commerce which might be the issue itself since it probably isn't played that often. Earlier today i had a 20 minute wait to find a strat 2v2 game which might say enough about larger games and how common those are.