I have re-enable the product ID field on the importer (if you can download v2.0.12+) of the import wp woocommerce addon.
The product ID field is enabled o the Template Fields step, in the Product Fields Group, click on enable fields and select product ID.
To make sure that you only update the SKU fields i would recommend under the permissions step, set the “Unique identifier” to ID , and disable the create and delete checkboxes, enable the update checkbox and set the import dropdown to “Only the following fields”, and set the fields textbox to “_sku”.
Then once ran the sku of your products should be updated.
Please make sure you have a backup of your website and database before running any import or exports so that you can easily revert any changes.