I would recommend creating a true/false field titled Active. If you set the default value on that field to true, it should automatically apply to all of your existing records. You can then set any invalid Department as active=false. Then, anywhere you reference Department, you can add a reference qualifier to only display Departments where active=true. If you want to take this a step further, you can update the module in the filter navigator so that it has active=true as the default condition for loading the Department list.
