A SQL Server Site / Project that has data associated with it cannot be deleted in the normal manner for deleting other data (deleting through the Output Views, or Data Tables).
The procedure to delete a Site / Project is as follows.
•Select File – Project/Site Association.
•Select the Project/Site
•Right Click and select Delete or Rename
If a Site or Project contains data you will need DBO access to delete the whole Site/Project from the database. The only other way to delete a Site / Project is to delete all data related to the Site / Project, then try to delete the Site / Project.