I have the same issue. Until very recently I could send a revised invoice irrespective of whether the buyer had already paid. Note; the most which could be revised was equal to the postage amount. The Ebay rep I spoke to swore black and blue the function never existed. 

I often need to do this as despite my having a flatrate policy (irrespective of the number of products purchased), Ebay adds postage for each item on a seemingly random basis. I would revised the invoice and refund the excess postage. Now I can't even revise the postage so have to cop fees on the amounts I have refunded.

The flatrate issue has been raised a few times and settings fiddled with by Ebay reps over the last couple of years. Nothing seems to work and the issue has been "escalated" but it's unknown when it will be fixed. In the meantime I get feedback that orders are abandoned due to my excessive postage.

The other solution proposed is for me to contact Ebay each time for them to manually adjust the customer invoice, and then manually place a credit against my Ebay account for the excess fees. The problem is everytime I need to deal with a rep who swears it's not possible and I need to escalate to someone who does. That's at least 40min's to a couple of hours of my time each time to get something like 80 cents to a couple of dollars refunded.