A merge itself moves no money: nothing is charged and nothing is refunded. If the customer paid shipping twice, Tacey records the duplicate as money owed back to them so it is not forgotten. The customer gets an email explaining their orders were combined, and you get one too unless you turn it off.
The money, step by step
The first order keeps its payment. Nothing is charged for the items added to it.
The second order is cancelled without a refund. Its payment stays, because those items are now shipping under the first order. In Shopify it shows as cancelled and still Paid.
Both payments stay exactly as they were. The Order Merge page puts it plainly: "No payment is charged when you confirm. Both orders keep their own real transaction, unchanged."
The duplicate shipping charge
If the customer paid for shipping on both orders, one parcel now goes out but they paid for two. Tacey works out the second order's shipping charge and records it on that order's ledger as:
Refund owed to the customer: $5.00. Not refunded yet. Issue it from this order in Shopify.
The order then appears under Action needed on Home and in Orders.
To refund it:
Open the cancelled (second) order in Shopify.
Issue a refund for the shipping amount shown in Tacey.
Tacey notices the refund on its next check and the order leaves Action needed.
Nothing is refunded automatically. You decide whether to return the shipping, keep it (for example if the parcel is heavier now), or contact the customer.
If neither order had a shipping charge to duplicate, nothing is recorded as owed.
Why Shopify's reports may look different
Shopify's own Sales reports may still count the second order's items as ordered, even though no extra payment was collected for them. The confirmation screen warns you about this before you merge. Tacey's merge record is the accurate account of what happened.
The customer's email
When a merge completes, the customer is emailed from your store:
Subject: "Your orders #1024 and #1023 were combined"
"We combined two of your orders into one shipment. Order #1024 is now part of order #1023, and everything will ship together under #1023."
"No extra charge was made and no refund was issued. Both orders keep the payment you already made."
It is written in the language the customer checked out in. If the order has no email address, no email is sent. Shopify's own cancellation email is not sent for the cancelled order, so the customer is not told their order was cancelled without explanation.
This email is only sent for a merge that fully completed, never for one that failed or only partly went through.
Your notification
Order merged notification, on the Order Merge page, sends an email to your store notification address every time a merge completes. It is on by default. Use Turn off to stop it. The address it goes to is set in Editing Tools → Global settings, under the email settings.
The same section shows whether your email sending domain is fully set up, for example "Sent from yourstore.com, which is fully authenticated (SPF, DKIM, and Return-Path all verified)." If some checks are failing, it warns that merge notifications may not arrive reliably.
What this does NOT do
It does not refund the duplicate shipping for you. It records it so you can.
It does not charge the customer for combined items.
Turning off your notification does not stop the customer's email.
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