If an order has been placed for an item that you have disabled/removed, there is most likely a product customization that shares the item's name, such as the option to add the item as an add-on. In this case, you will need to edit your product customizations.
To access product customizations, click on the menu and then select Product Customizations.
Once you are in your product customizations, locate the customization that includes the item. Edit the product customizations to either:
Remove the customization related to the item, or
Indicate next to the item that it is temporarily out of stock.
However, the second option will not remove the ability to still order the item.