let me edit my post after reading the one above mine, I can't adjust my order total, you will have to process the order then do a return paying twice one for the charge and once for the return.
Most if not all processors are set up on a charge per transaction so a charge is one (were the credit card is run)and a return is one (were a partial or full refund is given for the order) double pay for the one order.
O yea most processors charge more % wise for the return than the card run so be careful here.
Only way not to pay twice is contact the customer explain the order is not in stock ( first place this needs to be addressed, all out of stock items should be displayed "out of Stock") and then see if they want to complete the order less the item out of stock. You will need to get the credit card number and redo the order to reflect the item taken out, process the order with the new price and Do Not Process the other order.
Reading bwnbwn's post I think it depends on the platform you are running your store or a way you have a processor set up.
Sorry for my non-technical explanation ... but I literally have a button on store admin site "adjust order total", I type in new amount and press "accept". It has to be done however, before capturing the payment. We are using only Paypal Website Payment Pro as our cc processor. If we captured that payment we would have to do as bwnbwn suggested. Process order and then issue a refund.
Just to finish up the topic, I looked into Paypal further and found that it can be done directly through Paypal. As long as you just authorize the payment, instead of authorize and capture, Paypal gives you an "adjust order" button.
Msg#: 3618019 posted 1:41 am on Apr 4, 2008 (gmt 0)
Also, with PayPal payments, you can capture up to 115% of the authorized amount (can't exceed $75 extra, though). Nice feature to handle those orders where the customer wants to expedite shipping, or add-on a widget to their order.