Scott from another forum helped me with this query:
SELECT mt.BusinessUnit, mt.PartNum, mt.WONum, mt.TransDate, mt.TransQty, ISNULL(ot1.WOQty, ot2.WOQty) AS WOQty
FROM tblJDEWOData2 AS mt LEFT OUTER JOIN
tblWONumWOQty AS ot1 ON ot1.WONum = mt.WONum LEFT OUTER JOIN
tblHistory AS ot2 ON ot1.WONum IS NULL AND ot2.WONum = mt.WONum
ORDER BY mt.TransDate