When a job is marked as 'filled' in Matchmaker, it is necessary to then proceed to the 'Admin->Job Boards' section. The job marked as filled will not appear in the list that is displayed as only open jobs with a website comment and at least one skill are displayed here.
When the user presses 'Upload', the system is aware of any jobs that may have been previously on the list but are now marked as 'filled' and removes these from the website you are 'uploading' to. You will need to repeat this procedure with any other Job Board that the 'filled' job previously appeared on.
Once this is done it should not be necessary to manually remove any jobs from a Job Board.