Alterando o local padrão do conteúdo do WSUS através do comando wsusutil

 C:\Program Files\Update Services\Tools\wsusutil.exe /movecontent /help

movecontent command details: Changes the file-system location where the WSUS server stores content, and optionally copies any content from the old location to the new location.

movecontent <content path> <log file> [-skipcopy]

<content path>: The new root for content files. The path must exist.

<log file>: Path and filename of the log file to create.

–skipcopy: Indicates that only the server configuration should be changed and that the content files should not be copied.

C:\Program Files\Update Services\Tools\wsusutil.exe movecontent d:WSUS d:log.txt

Content location is being moved. Please do not stop this program.Content move has successfully finished.

fonte: http://technet.microsoft.com/en-us/library/cc720466(WS.10).aspx