Given the time frame, I am guessing you have solved this or found a workaround.
But for future reference: the site name is case sensitive! If my URL is: https://online.tableausoftware.com/t/sitename , my site can be 'SiteName' or 'Sitename' or any mix of upper and lower case. In the command line I need to make sure that I specify the site name using the correct upper / lower cases (e.g. tableau refreshextract --source-username username --source-password password --server https://online.tableausoftware.com --site SiteName)
Hope this helps,
Frazer, were you able to resolve the issue?