We use Paypal Payments Pro as our payment gateway, and have encountered issues capturing on an authorization when editing an order.
When editing an order Magento does not bring the payment information from Paypal into the new order, and don’t have the credit card info because it was submitted to Paypal directly through the API. As a work around, we simply select check/money order as the payment type, which allows us to create the order fine.
The problem is when it comes time to invoice the order; if the person processing orders isn’t paying attention they will forget that the funds need to be captured separately in Paypal.
As a solution, ideally the authorization from the original order would be maintained so that everything happens automatically like it does on an order that is not edited (cancelled and recreated). A secondary solution would be to at least display an alert when the order is invoiced if the payment type is check/money order so the person processing the order knows that the funds need to be captured.