On my second fight at the Freetown Arena the weapon and armour I used the first time round were missing from the chests.
Update: I reloaded from a quicksave and the items were back in the chests. The first time I just slept at an inn, and it didn't reset the chests.
Update: I reloaded from a quicksave and the items were back in the chests. The first time I just slept at an inn, and it didn't reset the chests.