I don't know how your have your file structure setup, but it may be an issue with the paths to the files in relation to the .htaccess file. Try just adding it to the .htaccess file in your public_html directory. That should effect all other directories globally.

If that doesn't work then there is way to do it with php, but if you have a bunch of files it would either mean creating a php file for each download you have, using an predefined list of files that can be downloaded and use url variables to choose which file, or to use a database to manage the files that will be downloaded.

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