If you are using Indie Commerce EDI and have imported the order into IMRCHNT, you can easily cancel the entire order by changing the Order State on the Customer Order to COMPLETED.  Once the web order importer runs again, it will send a cancel notice back to the website.  

If you want to cancel one item from an order, just mark the item as completed in the Customer Order.  Once the web order importer runs, it will send a cancel notice on that one item.  Then complete the rest of the order as usual in IMRCHNT by selling it through POS to complete.  

Which Types of Orders Can you Refund / Cancel in IMRCHNT?

- If all items are canceled, IC will cancel the order automatically and issue a refund.  The order status will be moved to 'Canceled' and a refund transaction will be initiated. Store will see an admin comment on the order about the refund.

- If the order is only partially canceled, say one of two items canceled, the order will be marked complete, once IC receives an ASN for all items. Partial credit Is not automatically triggered. Something needs to be done on the web site to issue the refund. Store will have to edit the order, remove the canceled item from the order and issue a refund from the website.  

Confirm your web tender allows for refunding, by checking if this option is enabled.