Rename your Configuration Manager Primary Site. Once you have installed your Configuration Manager Primary Site it is not possible to change it name. But what if you made a mistake or your company changes it’s naming conventions?? Well there is one way to change it. First off all stop the SMS_EXECUTIVE Service. After that open the site control file (<Installation directory>\Microsoft Configuration Manager\inboxes\sitectrl.box\Sitectrl.ct0) and search for BEGIN_SITE_DEFINITION. Close to that you will find your Primary Site name and you can change it (do not change anything else!!). After this save the file and start the SMS_EXECUTIVE Service again. Then after a few site refreshes your Primary Site name wil be changed.
In some cases it could be possible that you also have to change the value of the regkey: