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It seems that and empty .htaccess file is generated even after deleting the empty file in all my cpanel accounts.

Does anyone know what script in cpanel does this?

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This issue will occur if FrontPage is enabled.

Also please check /root/cpanel3-skel, to see if the .htaccess file is generated as per the skeleton.

Also, if the .htaccess file is blank, it doesn't do any harm.

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Neither of these are the case and it just showed up randomly. I will keep an eye on it to see if it happens again. Any other way it could show up? –  Chris Muench Apr 25 '11 at 22:04

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