Suppliers short-ship, and sometimes a delivery is taken in through Shopify rather than against the purchase order. Either way the order keeps showing units as incoming in Shopify until you settle it. Here is how.
Cancel the rest, or close the order
Suppliers short-ship. When you know the remaining items will never arrive, you have two ways to settle the order - both remove the missing units from the order's totals and stop them showing as incoming in Shopify:
Cancel remaining on one line - on an ordered or partially received PO, every line with items still outstanding carries a small ✕ button at the end of its row, beside the line total - hover or tap it for Cancel remaining, then confirm. The cancelled units drop out of the totals, the line keeps a "cancelled" note for your records, and the rest of the order stays open. Swapping in a substitute? Pair it with Add items.
Close the whole order - under More actions, click Close. Closing an order with outstanding items asks you to confirm, then cancels everything still unreceived the same way.
Stockroom also asks at the natural moment: when a delivery leaves items outstanding, an Items still on backorder prompt offers Keep open (another delivery is coming) or Close order (the supplier won't ship the rest).
Cancel remaining can't be undone - if the items do arrive later, add the product back with Add items and receive it. Close is different: a closed order can be reopened, and what closing took off comes back with it. And if MyWorks Sync is connected, the reduced quantities sync to QuickBooks automatically.
If the delivery was received in Shopify instead
Some stores take deliveries in as a Shopify transfer rather than receiving them against the purchase order here. That adds the stock in Shopify, but the purchase order stays open - so its units keep showing as incoming in Shopify for a delivery that already arrived, and Shopify gives you no way to edit incoming from the admin.
Stockroom watches for this. When a Shopify transfer receives items from an open order at the same location, the order shows Items on this order were received in Shopify, names the transfer with the units it took in and the date, and links to it with View transfer. If that covers everything the order still had outstanding, the notice also offers Close order, which takes those units back out of Shopify's incoming stock. If only some of the items arrived that way, the notice tells you what it found and leaves the order alone - a delivery that is still coming should not be cancelled.
Closing an order this way records no receipt in Stockroom, so that delivery's costs live in Shopify only. If you want landed cost and cost of goods tracked here, receive against the purchase order in Stockroom instead of creating a transfer for it.
Good to know
A closed order can be reopened, and what closing took off comes back with it - see Fix a delivery: undo a receipt, correct costs, change dates, reopen.
Cancelled units drop out of the order total and stop showing as incoming in Shopify; if MyWorks Sync is connected, the reduced quantities sync to QuickBooks.