Within a customer's order you are able to increase or decrease quantities of stock, remove items, suggest a replacement or fully cancel the order. You would do this by clicking into the customer's order and choosing order modification. You can also reach out to the customer through the messaging system if you prefer to speak with them about modifications first.
However, to avoid this situation altogether and be in good standings with retailers we recommend you consistently keep your stock updated and fulfill orders exactly as the customer places them.