Sometimes, an eBay buyer will want to return an item you shipped from FBA, or they will cancel an order.
If you're not able to log in to Amazon to cancel fulfillment in time, you should just communicate with your buyer and treat the order as a return.
You'll want to go to your Amazon Seller account, create a RMA (return) for the item, and it will give you a PDF to print. Then, email that PDF to the buyer, and tell them to stick it on the item and ship the item out to Amazon.
When Amazon confirms that they have received the item back, you will need to process the replacement order or refund manually. If you are processing a refund, login to PayPal and refund the buyer's transaction. Also be sure to cancel the order from "My eBay" to ensure that you are credited back the Final Value Fee from the sale.