If a pickup order is eligible for an automated conversion, you will see a "convert to ship" button above the line items on the order summary page, where you land when you click on the order number from the order list page (do not click the edit pencil on the order).
Once you click the Convert to Ship button, select the shipping address for the customer (you will see a link to the customer's entire saved address book, and you may enter a new address as needed), then select a shipping method, select a shipping rate, and indicate whether you would like tax to remain the same or for tax to automatically recalculate based on the order changes.
Finally, if you would like the system to automatically email the customer, modify the email as well.
The order will recalculate with these changes at the bottom of the page, where you can see if there will be additional charges or refunds to the customer when the order is processed.
You may submit the order and send your email, or just submit the order. When you submit the order, the order will be captured (any balance due will be fully captured, or if the order modifications resulted in an over-charge, the balance will be refunded). The order will be converted to a ship order, but it will retain the same order number.
If the order is not eligible for conversion, you will need to cancel this order and re-place it as a ship order. As for the charged credit card, you can either void/refund the charge on this order and recharge the new order amount on the new order, or you can leave the charge on this order even though the order is canceled, and charge only the additional shipping amount (adjusted for whatever tax adjustments are required, if any, as a result of changing from pickup to ship). If you choose the latter, be sure to make a note on your order that the balance was charged on such and such a date on order number XXX, with an explanation - just in case someone needs to audit this later.
If you need additional help with this please contact your Account Manager, or Customer Support, whose information you can find at the top of the Settings section in your Nexternal Order Management System.