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Is it possible for the shipping rate rules to be applied after a discount has been applied to an order?

That is a good question and unfortunately the answer is no. Shopify has set up carrier rates (rates provided by an app or third party) so they are based on the total value of the cart, before any discounts are applied.

Because of this it's not possible to apply rate rules to the cart value after the discount has been applied. We suggest you consider this when setting free-shipping thresholds and other rate rules.

If you'd like to see Shopify add this feature why not let them know?
Contact Shopify