Then you can make a list of IDs you want to delete,
SELECT mlsdb.virtualdb.mlsnum
FROM mlsdb.virtualdb LEFT JOIN mlsdb.mlstable
ON mlsdb.mlstable.ListID = mlsdb.virtualdb.mlsnum
WHERE mlsdb.mlstable.ListID IS NULL
and delete 'em,
DELETE FROM mlsdb.virtualdb WHERE mlsdb.virtualdb.mlsnum
IN ( <your_list> )