When I run the VisitorGenerator plugin from commandline using

I get the following error:

Fatal error: Call to a member function subDay() on a non-object in /path/to/piwik/plugins/SitesManager/API.php on line 1198

I did some back tracking and found the cause to be the dates variable passed into invalidateArchivedReports has a line-break at the end so it puts the date into invalidDates instead of toInvalidate.

I believe that:

$dates = explode(',', $dates);

should be:

$dates = explode(',', trim($dates));