I have the same issues but added another. What about those auctions that close before the increase and you don't receive payment until afterwards? The easy way for me was to check the USPS rates and increase the handling fee to cover the rate difference for auctions that will close before the increase and/or I can't ship until afterwards (i.e. most of my auctions close on a Friday so I can't ship until Monday which is the first day of the increase) so eBay's calculated shipping will be wrong so that's why I increased the handling fee. The eBay note I received from eBay was that you could adjust the shipping rates in live auctions... but you have never been able to do that before with a bid on something.
The don't pay until you send a new invoice is a tough one since the Buyer has agreed to pay whatever your auction states and will likely rant if you add on the increased amount later. Actually, the increase looks to be spread nicely to cover all the major eBay shipping options... like Priority Flat Rates, First Class and Media Mail. I bet the USPS joined in with eBay to see how we were shipping and adjust accordingly.
It would see to me that you're stuck for the difference if you don't put in some additional handling fee because you can't control when someone will make the payment. If they use PayPal and you can ship at the old rate refund them the difference and put a postive note in your auction like... I have added a small handling fee to cover the new USPS rates and will gladly refund it if your payment allows me to ship prior to the effective date of the increase on May 14th.
Just some thougts... not many answers