Those customers who pay immediately and don't wait for the revised invoice, probably don't care that they are paying a bit extra in postage.

My strategy now is to only refund if the overpaid p&h is way more than the postage, packaging and handling actually cost but now I take out the 9.9% FVF paid on that postage and refund what is left.

You don't get a defect for partial refunds due to overpaid p&h. At least I haven't yet and I make around 10 refunds per week. Unfortunately my products are almost always purchased in multiple quantities so I often find buyers purchasing 10 items, not waiting for revised invoice but paying immediately. I gotta say I'd rather get that immediate payment - if they haven't paid immediately, it is so easy to forget to pay at all.