Print the first label, then go back to the sold item, and choose* "print another label" from the "more actions" dropdown on the My eBay Sold page, which will bring up the label dialog again where you can change the weight and size and print a second label.
*If using Selling Manager it's "Print Shipping Label" under the actions dropdown, if using Seller Hub/Selling Manager Pro, dunno)
Be aware that that will attach 2 tracking numbers to the sale which MAY cause some side issues - I leave that to other posters here with more expertise in that area of policy and disputes. (with USPS multi label shipments it is often recommended to print a second label via PayPal shipping and not upload the tracking, particularly if second label is printed much later and will cause a late shipping ding - that's not an option with FedEx labels though)
