Was this a Best Offer? Tricky because one of the rules of Best Offer is that shipping discounts are not included in the offer.
For example, I could offer $10 each on 10 items that you have priced at $20 plus $10 shipping, and the offer would be read as $100 price plus $100 shipping.
So your counter offer should either make it clear that there will be no shipping discount OR offer a further discount on the asking price to allow for the shipping. Which is wierd, but Best Offers are not commonly on quantities of products.
Oh and you can revise the invoice after the buyer has purchased but not paid, or refund him part of his payment to allow for a shipping discount.l