does not do the same behavior as when I click "save permalinks" manually

[shaktimanpurush]

hi,

Sometimes I have issues on my woo-archive page with WPML, and only pressing "save permalinks" button manually solves this.
WHen I use this plugin, it does not have the same effect as pressing "save permalinks" manually.
When I have a custom comment inside the .htaccess #wordpress, this is only remove by pressing "save permalinks" manually, not by this plugin. I have disallow_file_mods on "true" in my wp-config.php for security.

Can you clarify on why this is ?

Thanks