I had an order in which the payment was processed.
Now I have to change one of the options selected to an upgraded option. This will add more to the invoice amount.
Two problems encountered.
1. I edit the order from my administration panel. I select the upgraded option and click recalculate. The extra option amount does not get recalculated at all. So I manually change the price in the price box.
2. When I get to the 3rd page “Totals”, the total amount shows for all the goods. The next step “Summary” is where I can enter the credit card info and process payment.
I guess what I am getting at is if I were to process this payment, the whole amount would be charged (again), not just the extra added amount.
Can I not edit an existing order and either credit or debit the customers card depending on whether the customer adds or deducts products??? 
I would think this is a very common occurrence.
Any comments?
We can adjust the total in the store but if we want to modify (+/-) an already paid for amount then we have to log in to our merchant account and adjust it there to match the store.
Of course my most used store is still on 1.3.5 which will be upgraded to 4 (soonihope).
I've never had a store that made credit purchase adjustments. that doesn't mean it can't be done, I've just never done it. If you have a terminal in your office that is linked to your merchant account you can adjust from there as well as long as they are linked.