MSSQL:actualice las filas coincidentes del archivo cargado

Este es un enfoque mucho más fácil para acceder a los datos delimitados por conductos. Encuentra sus datos tipo tabla dentro de #temp2. A partir de aquí debería ser fácil UPDATE ,INSERT o MERGE sus datos en su destino.

Atención:podría adivinar el significado de sus columnas, por lo que los nombres de las columnas podrían ser basura...

CREATE TABLE #temp1(WHOLEROW VARCHAR(8000));
INSERT INTO #temp1 VALUES
 ('F20160323-1000|FSI|BISCOCHO|DELIVERED|42317|||||GINA T|TENANT|42311')
,('F20160323-1001|FSI|MARTINNE|DELIVERED|42314|||||MERLIE STRADA|IN LAW|42311')
,('F20160323-1002|FSI|MANALO|DELIVERED|42313|||||GINA A|TENANT|42311')
,('F20160323-1004|FSI|HAMOY CAJAYON|DELIVERED|42311|||||MERLIE QTRADA|IN LAW|42311')
,('F20160323-1003|FSI|FRANCISCA|DELIVERED|42312|||||GINA B|TENANT|42311')
,('F20160323-1005|FSI|NINA|DELIVERED|42318|||||MERLIE STRADA|IN LAW|42311');

;WITH Splitted(AsXml) AS
(
    SELECT CAST('<x>' + REPLACE(t1.WHOLEROW,'|','</x><x>') + '</x>' AS XML)
    FROM #temp1 AS t1
)
SELECT AsXml.value('x[1]','varchar(max)') AS ID
      ,ID_Splitted.*
      ,AsXml.value('x[2]','varchar(max)') AS FSI_Field
      ,AsXml.value('x[3]','varchar(max)') AS CAPTION
      ,AsXml.value('x[4]','varchar(max)') AS STATUS
      ,AsXml.value('x[5]','varchar(max)') AS NUMBER
      ,AsXml.value('x[6]','varchar(max)') AS Fld1
      ,AsXml.value('x[7]','varchar(max)') AS Fld2
      ,AsXml.value('x[8]','varchar(max)') AS Fld3
      ,AsXml.value('x[9]','varchar(max)') AS Fld4
      ,AsXml.value('x[10]','varchar(max)') AS TARGET
      ,AsXml.value('x[11]','varchar(max)') AS TARGET_TYPE
      ,AsXml.value('x[12]','varchar(max)') AS TARGET_NUMBER
INTO #temp2
FROM Splitted
CROSS APPLY(SELECT LEFT( AsXml.value('x[1]','varchar(max)'),1) AS FirstLetter
                  ,CAST(SUBSTRING(AsXml.value('x[1]','varchar(max)'),2,8) AS DATE) AS IncludedDate
                  ,CAST(SUBSTRING( AsXml.value('x[1]','varchar(max)'),11,100)  AS INT) AS IncludedNumber) AS ID_Splitted;

SELECT * FROM #temp2;

DROP TABLE #temp2;
DROP TABLE #temp1;

El resultado

ID         FirstLetter  IncludedDate    InclNmbr    FSI CAPTION      STATUS     NUMBER  TARGET          TYPE    NUMBER
F20160323-1000  F       2016-03-23      1000        FSI BISCOCHO     DELIVERED  42317   GINA T          TENANT  42311
F20160323-1001  F       2016-03-23      1001        FSI MARTINNE     DELIVERED  42314   MERLIE STRADA   IN LAW  42311
F20160323-1002  F       2016-03-23      1002        FSI MANALO       DELIVERED  42313   GINA A          TENANT  42311
F20160323-1004  F       2016-03-23      1004        FSI HAMOY CAJAYONDELIVERED  42311   MERLIE QTRADA   IN LAW  42311
F20160323-1003  F       2016-03-23      1003        FSI FRANCISCA    DELIVERED  42312   GINA B          TENANT  42311
F20160323-1005  F       2016-03-23      1005        FSI NINA         DELIVERED  42318   MERLIE STRADA   IN LAW  42311