If you are currently having issues with an SKU not updating, this has been caused by an issue with the clone/duplicating plugin on your website. In the most recent versions of Woocommerce (Ecommerce Functionally), this has caused Woocomerce functionally issues.
If you have access to your website's plugins, please remove any other duplicating tool and install https://wordpress.org/plugins/woo-easy-duplicate-product/. This is the only plugin that works, for duplicating products the proper way. Please Contact Ubie Support for us to resolve this issue on your website.
This is currently an ongoing investigation, to find a solution for updating existing products that have used the duplicating tool causing the issue. Currently, the product would need to be removed and started from fresh to solve the issue.