If a a auction winner has won multiple auctions from you, and has not yet paid for the items, and you want to combine shipping you will need to send the user a invoice.
To send an invoice please see this guide:
The steps are: go to "My eBay" find your transactions under "sold" and to the far right under actions (you may need to click on 'more actions') select the "send invoice" option.
On the send invoice screen simply adjust the shipping amount to your desired value and click send. The auction winner will then have to pay via the invoice form. A common question a seller might have after this is will eBay recognize the new shipping amount and charge you, the seller, according to this new amount when calculating final value fees rather than the previous amounts listed in the separate auctions? The answer is yes, eBay will charge you based on the new adjusted fee in your invoice so long as the buyer pays via the invoice.
If a buyer has won multiple auctions and paid for them individually before you could send a invoice with a new adjusted shipping amount, here are your options:
You can give a partial refund via paypal - or refund the purchases completely, however eBay will still recognize that the buyer paid for the auctions seperatly and charge the seller accordingly.
For example if a bidder won 3 auctions, each with a shipping cost of $5.00 each, and paid for each auction individually - before you could combine shipping costs, eBay will charge the seller for $15.00 worth of shipping at this point.
If you want to combine shipping of those three auctions to $5.00 total instead of $15.00, you can offer a partial refund for $10.00 back to the auction winner, but you as the seller will be absorbing fees for monies you did not receive. You may want to offer the amount you intended to save the auction winner on shipping minus those fees, which can be tricky to calculate the exact amount, please see the link below on how to find that value.
Final Value Fee Calculation:
Alternatively, you could cancel the auction via the resolution center (found here: http://resolutioncenter.ebay.com/ ). As a seller once you initiate the cancel auction request, the auction winner must also agree. Once done, you can relist the auction and try again, this time winner bidder will want to wait for a invoice with combined shipping.