You can perform a site reset of a Configuration Manager 2007 site server by starting Configuration Manager Setup from the site server computer's Start menu or from the Configuration Manager installation media.
To perform a site reset
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Close any open Configuration Manager console connections to the site server.
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On the primary site server computer, click Start, click All Programs, click Microsoft System Center, click Configuration Manager 2007, and click ConfigMgr Setup, or navigate to the .\bin\i386 directory of the Configuration Manager 2007 installation media and double-click Setup.exe.
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Click Next on the Configuration Manager Setup Wizard Welcome page.
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Click Perform site maintenance or reset this site on the Configuration Manager Setup Wizard Setup Options page.
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Select Re-apply default file and registry permissions on this site server on the Configuration Manager Setup Wizard Site Maintenance page.
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Click Yes in the site reset confirmation dialog box.
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Configuration Manager Setup performs the site reset process.