Oh I think I can potentially explain that one. Arenthia is one of those places that has different phases depending on what stage of the quest you're on. From a distance, it's always set to one phase, but it may change phases when you actually enter the Arenthia city "cell". So you're seeing the chest in one phase, but the chest isn't there in the phase you actually enter (due to it either having already been taken in that phase, or just not existing).