Rename Configuration Manager Primary Site. Once you have installed your Configuration Manager Primary Site it is not possible to change its name. But what if you made a mistake or your company changes its naming conventions?? Well, there is one way to change it. First of 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 will be changed.
In some cases it could be possible that you also have to change the value of the reg key:
HKLM\Software\Microsoft\SMS\Identification
NOTE: Keep in mind that editing the sitectrl.ct0 is not supported by Microsoft!