If you are one of these players, please know that your items have NOT been deleted or removed, they are simply no longer visible. To access items stored beyond the 4,000 visible slots, you will need to make room by removing some items currently displayed.
Please note that some items do not fall into a specific category tab in your inventory. You may need to search for the item under 'All.' The Medieval Tower is one example of a building you will only find under the 'All' tab.