Adjusting Order Quantities in Magento

Answer 1

If the order is fresh, (e.g. no extraordinary history to track), you could "edit" the order. That will actually cancel the first record and create a new one where you can reflect correct shipping, quantities, etc.

You would need to request their payment data again if they used a credit card, but if you're contacting the customer anyway, that's a perfect opportunity to get it done.