Unintentionally I checked out the C:\ hard drive to get controlled by SVN.
Result : All of the sub folders are version controlled.
How can I remove the relation of the C: folder to svn without deleting anything?
If you SVN is 1.7+ (one .svn folder in the root of WC) just delete C:\.svn\ folder
Open View > tick on Hidden Items to look for the folder