To delete an existing web publication, select the respective web publication from the WebPublisher. The following options are then available:
Delete the site files
The files of the web publication on the hard drive are deleted; this includes models, images, scripts and any other publication files.
Publications that share files with the publication to be deleted are also affected and may no longer function.
Delete the website in IIS
Select this option if you want to remove the entire website also from the IIS.