I'm trying to update product urls, but the import functionality in Magento 2 adds new item id into cataloginventory_stock_item table for each updated sku and I have to manually delete each duplicate from the table. Does the import update csv require more than sku and url_key? Could that be the reason?

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The only one required column for CSV is "sku" (http://docs.magento.com/m2/ce/user_guide/system/data-attributes-product.html). Please, check if you are using "Add/update" option when importing.

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