Du kan prova att placera gruppen inuti en underfråga och sedan gå med med "JobOrderID", så här:
UPDATE J
SET J.StatusID = A.statusId
FROM MKT_JobOrder J
INNER JOIN (
SELECT J.JobOrderID
, CASE
WHEN SUM(DUV.VendorDUQuantity) = SUM(RD.InvoiceQuantity)
THEN 1
ELSE J.StatusID
END AS statusId
FROM PLN_DU_Vendor DUV
INNER JOIN ENG_Release R ON R.ReleaseID = DUV.ReleaseID
INNER JOIN ENG_DU_Header H ON H.ReleaseID = R.ReleaseID
AND DUV.DUID = H.DUID
INNER JOIN MKT_JobOrder J ON J.JobOrderID = R.JobOrderID
INNER JOIN MKT_CustomerOrder CO ON CO.OrderID = J.OrderID
LEFT JOIN PMT_RFDHeader RH ON RH.JobOrderID = J.JobOrderID
LEFT JOIN PMT_RFDDetail RD ON RD.RFDID = RH.RFDID
AND RD.DUID = DUV.DUID
WHERE CO.OrderID = 100
GROUP BY J.JobOrderID
, J.StatusID
) A ON J.JobOrderID = A.JobOrderID