The warehouse is where players can store their unused items for future use.
Items won as rewards from quests or from minigames are automatically placed in the warehouse. Items already on the cafe also go to the warehouse when it is dragged to the warehouse portion, or anywhere outside their cafe.
Currently, there is no limit as to how many items a user can store on their warehouse.
Also, disappearing items from the warehouse are highly uncommon, but not impossible. Should such a thing happen, scroll down to the bottom of the page and click 'Contact Us' to file your report, or post in the Technical Issues/Bugs section of the Cafeland forum with your Facebook ID.