You can disregard that displayed message. Your root .htaccess file is locked so that is why you are seeing that message. Permalinks are internal in WordPress itself and are not created in .htaccess code/files. What WordPress is trying to do here is a friendly reminder, but in this case you can disregard the message because it does not apply when you have BPS or BPS Pro installed. BPS creates the standard WordPress .htaccess code that is required for custom permalink rewriting and of course contains all the BPS security filters combined into the standard WordPress Rewrite .htaccess code for custom permalinks.
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