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 At one time in setting up the .htaccess maker, I added a line to the "Exceptions / Allow direct access to these files" section. It was actually a problem, so I removed it. But every time I rerun .htaccess Maker, it replaces the entry in the actual .htaccess file. It no longer appears in the backend UI, but it does appear in the generated .htaccess file.

In my case the subdirectory was "forum", as I run a Kunena forum. I was trying to get the SEF URLs working with Kunena, and I mistakenly added the entry. Now it won't go away.

This is also happening with "affiliate" which I added as a test, again mistakenly.

Somehow, .htaccess Maker still remembers those lines added, and keeps putting them in, even though they have been removed in the backend UI.

Here is the relevant text from the generated .htaccess file:

##### Advanced server protection rules exceptions -- BEGIN
RewriteRule ^administrator\/components\/com_akeeba\/restore\.php$ - [L]
RewriteRule ^administrator\/components\/com_admintools\/restore\.php$ - [L]
RewriteRule ^administrator\/components\/com_joomlaupdate\/restore\.php$ - [L]
RewriteRule ^affiliate/ - [L]
RewriteRule ^forum/ - [L]
##### Advanced server protection rules exceptions -- END

Attached is a screenshot of the UI section, where you can see the lines are not there.

Thanks.

OK, I figured it out. There is more than one section of the UI that adds lines to that section in the .htaccess file. I thought the paragraph separation meant a different section.

Nevermind.

Thanks.