According to Amazon’s Terms of Service, we cannot send shipment notifications for orders placed through Amazon. This is also the case for orders that are imported through other channels or any other orders that contain an email address ending in ‘marketplace.amazon.com’.
These customers should still receive an email from Amazon, as soon as the shipment information is sent back to Amazon indicating that the order has been shipped.
However, pelase note that this only applies to shipment notifications. Emails can still be sent for these orders using automation rules or sending manually a generated return label. Either way, there might be a chance that your customers will not receive these emails. For further info, you might have to contact Amazon directly and ask if these actions follow their Terms of Service.