Shipping outside Shopify

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I have a short term super discount for my business from a shipper.  I can not apply this discount in the Shopify store as I won't know the amount during purchase of product.  Can I:

1. Let my customers purchase the shipping on Shopify as calculated.

2. Without printing shipping label or shipping, list the order as fulfilled.

3. Run the shipping through my discounted method outside Shopify and ship.

4. Collect full amount paid in Shopify, including full shipping paid.

5. Send my customer the calculated difference of my offsite discount, or give them a discount on next order?

 

I am unsure if shipping paid is not fully used as in above, what happens to shipping funds if not used? Does it go to seller on fulfillment of order, or can it only be held in limbo until refunded through Shopify (can only be sent to shipper)?

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