Partially refunding an order doesn't update the quantities in the Order Export and Invoices

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We are a recent Shopify user (in the past few months).

I have one major issue with the platform that I haven't figured out a way to deal with.

We have lots of orders & times where based on the nature of our business some items in our online store become unavailable because we work in overstock & 'end of line' merchandise - sometimes when you go to the shelf - the item just isn't there & can't be reordered and we have to refund parts of orders (note our average order is for between 15-20 items & we might have to refund 1 or 2 items).  This seems to work great in the "Orders".

But then we want to produce reports for which products to pull etc and using the Order Export, it includes the products we have refunded (and makes it look like they are still on order).  This stunk - but temporarily I got over it and now we manually handle everything (i.e. the ups and downs of the order line items).

 One suggestion is to cancel and reinput the order... but that means inputting 100's and sometimes 1000's of orders back into the system where we have over 2000 sku's (many of which are similar & increases likelihood we will misinput a customers order).  It also means that the customer will get a cancellation email & a new order email etc. that is a hot mess.

Then another issue arose, I installed the Order Printer (free) to be able to print invoices for all my customers - and then I was going to look into one that would email invoices automatically instead - but figured I would start with Order Printer.  We when I produce invoices with Order Printer - it doesn't update for refunded/restocked products either.  So if I had an order for 25 items and 1 for $1000 has to be refunded... the invoice doesn't reflect the refund.  

Am I nuts or is there something wrong? Are there any 'extra' apps that are able to work with Shopify's partial refunding process & not screw up order exports / invoicing?  

Why wouldn't updating an order actually remove the item/charge from the order for exports / invoices? 

If there is help out there, thanks in advance.

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Found another place that it doesn't work.

The fulfillment notice to a customer shows "Refunded" in the line item and the quantity that is shipped.  But in my test where I had a customer order 3 & refunded 2 - it shows x 1 or 3 and then the word "Refunded" underneath.

Then if the person clicks on "View your order" for clarification - it shows them their original order as if no adjustments had been made at all.

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