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Hello @jerry0000,
Thank you for contacting Rank Math support.
We do run the function wp_cache_flush() in the plugin to flush the permalinks for the Remove Category Base and other features to modify the permalink structure of WooCommerce products, but that happens inside the rewirete_rules_array filter, so this shouldn’t cause any issues with the site’s performance.
Please do not hesitate to let us know if you need our assistance with anything else.