Update , Select and Join using 3 tables
I guess you don't want (for every Tracks.prefix) a new row to be inserted but the existing row to be updated (otherwise you would get collisions on the primary key of Tracks). You can this query to check first what will be changed:

SELECT 
    tr.prefix,
    tr.label_id AS existing_label_id,
    top.label,
    lbl.label_id AS new_label_id 
FROM 
    Tracks AS tr
  JOIN
    Top100 AS top  ON top.prefix = tr.prefix
  JOIN
    Label AS lbl  ON lbl.label_name = top.label ;


and then update:

UPDATE
    Tracks AS tr
  JOIN
    Top100 AS top  ON top.prefix = tr.prefix
  JOIN
    Label AS lbl  ON lbl.label_name = top.label
SET
    tr.label_id = lbl.label_id ;