All SKUs in QuickBooks Online and WooCommerce must be unique for linksync to work without issues.
QuickBooks Online does not require each SKU to be unique, meaning you can have multiple products with the same SKU in QuickBooks Online. This is bad news for WooCommerce, where every SKU must be unique.
Note: In the event you have duplicate SKUs in WooCommerce, only one of those SKUs will be correctly synced to QuickBooks Online.
What if I have duplicate SKUs in either or both systems?
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