We print the approved label attached to the SKU on the order. A new upload does not change bags that already went to the roaster.
Check these
The new label is approved in My Custom Products — not pending or rejected. Custom label approval status
The Shopify (or other store) product is still mapped to the new custom-product SKU, not the old one.
You did not leave an old custom product imported on that listing.
If you replaced a label, remove or stop selling the old custom product so new orders cannot pick it up.
If a test order already shipped with the old file, place a new test order after the new label shows approved.