In this case the cleanest way is to simply ship the missing unit to the buyer as quickly as possible using the same shipping address, then message them politely through Buyer-Seller Messaging to let them know it’s on the way and provide the tracking if available, since Amazon doesn’t have a built-in tool for partial reshipments on FBM orders. You don’t need to reprint the invoice in Seller Central or create a new order, just keep your own record by noting the order ID and adding a copy of the shipment receipt or tracking in your files in case Amazon asks for proof later. This way the buyer gets what they paid for and you protect your metrics by showing good customer service.
Buy a new shipping label for the missing item. You must do this outside of the original Amazon order.
Use a tracked service (like Royal Mail Tracked 48, Evri, etc.). The cost of tracked shipping is a small price to pay for seller protection.