I usually refund the postage on the items that have excess postage on them, so that I'm not refunding any of the purchase price.  I get a lot of buyers who pay for combined items before they receive an invoice.  I haven't had any problems with paypal or ebay because of the amount of refunds I do, but I always make sure I never refund from the purchase price.  If they make two separate payments and I have to refund more than the postage on one payment, I refund some from both payments.

I have a blurb in my description and on my shop page that effectively says the combined rates displayed in my shop only apply if they wait for an invoice for multiple items before they pay.  If they pay without waiting, I refund the excess postage minus the fees I've already paid on it.