To stop selling a specific SKU so it no longer appears for orders:
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Go to Inventory > Mass Edit.
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In the "Select Field to Edit" dropdown, choose "Stop Selling".
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In "Limit to SKU/Description/Location", enter the full SKU you want to stop selling, then click GO.
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Toggle the "Stop Selling" option for the SKU you wish to stop.
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Click Save.
Click here for a video on how to Stop Selling a Specific SKU