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db<>fiddle
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create table J_CordToolARCCutSheetPlanning(JobNumber int, LotNO varchar(20), SerialNo int, TrackingNumber int);

insert into J_CordToolARCCutSheetPlanning values
(1234 , '199111 -001' , 40001 ,0),
(1234 , '199111 -001' , 40033 ,0),
(1234 , '199111 -004' , 40050 , 0),
(1234 , '199111 -004' , 40051 ,0),
(1234 , '199111 -008' , 40111 ,5),
(1234 , '199111 -008' , 40112 ,5);
6 rows affected
UPDATE
J_CordToolARCCutSheetPlanning
SET
J_CordToolARCCutSheetPlanning.TrackingNumber = CASE WHEN t.trackingNumber != t.max_trackingNumber THEN t.max_trackingNumber + t.seq ELSE t.trackingNumber END
FROM
(SELECT *,
DENSE_RANK() over(ORDER BY t.LotNO) AS seq,
(SELECT MAX(trackingNumber) FROM J_CordToolARCCutSheetPlanning) AS max_trackingNumber
FROM J_CordToolARCCutSheetPlanning t
WHERE JobNumber = '1234') t
WHERE J_CordToolARCCutSheetPlanning.SerialNo = t.SerialNo
6 rows affected
select * from J_CordToolARCCutSheetPlanning
JobNumber LotNO SerialNo TrackingNumber
1234 199111 -001 40001 6
1234 199111 -001 40033 6
1234 199111 -004 40050 7
1234 199111 -004 40051 7
1234 199111 -008 40111 5
1234 199111 -008 40112 5