I partially refunded an order, and then fulfilled it. It's still giving me a notification even though all the steps have been taken (packing slip, label and archive) have already taken place. The notification is showing in the app and on the web platform.
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If you're referring to the notification badge that appears in the admin and in the app to indicate that you have an order, then this would come from "open" orders. Open orders are non-archived orders so in order to remove the notification badge, you'll need to first archive the order. If you go to the "Orders" section of your admin, then click the small white box next to the order number, then "more actions" you'll see the option to archive the order.
That should do the trick; however, if not, then feel free to post a screenshot of what you're referring to as I'd be happy to take a deeper look.