Amazon's fulfillment fees depend on the order's fulfillment status and the applicable Amazon policies. Cancelling an FBA/MCF fulfillment does not necessarily mean that all related fees will be waived or refunded.
For accurate information about fees associated with a specific order, check the order and transaction details in Amazon Seller Central or contact Amazon Seller Support.
The Shopify order cancellation setting in Shipr only controls whether Shipr updates the Shopify order status after a successful Amazon fulfillment cancellation. It does not control Amazon's fees.