The quest chest that is part of the Lost Refuge quest is present every time the zone is loaded. Other quest-associated chests, such as for Erza’s ledger, disappear after the quest has been completed.
Since leaving a zone (via portal or way point) resets that zone, this currently creates an easy and safe source of early gear and gold. Even if/when zone permanence is introduced, the chest is near a waypoint so being able to reset the zone in any way means this chest will be lucrative early on in the leveling experience.