I already have an .htaccess file, and I'm not sure how your Htaccess plugin will work with it

If the file exists and there is a Directive block in it, the plugin will add the settings of this block to the settings page and after saving the changes it will update only the Directive block in the existing .htaccess file.

This article related to Htaccess plugin

Additional resources: Htaccess - User Guide

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