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Incorporando uma instrução sql case em uma consulta sql que está usando FOR XML


Acho que inserir a expressão case original no local correto deve funcionar. Tente isto:
PROCEDURE [dbo].[CreateLandingPurchaseOrderDetails]

-- Add the parameters for the stored procedure here
@startDate DATE, @endDate DATE

AS
BEGIN
    -- SET NOCOUNT ON added to prevent extra result sets from
    -- interfering with SELECT statements.
    SET NOCOUNT ON;

    -- Insert statements for procedure here
    SELECT (
       SELECT
            Contacts.ContactId AS '@ContactId',
            LandingHeaders.VesselOwner AS '@Owner',
            FORMAT(SUM(LandingDetails.Quantity * LandingDetails.UnitPrice), 'N2') AS '@Owed',
            SocietyMemberships.WeeklyDeductionRate AS '@WeeklyDeductionRate',
            SocietyMemberships.FromMinimumReturn AS '@FromMinimumReturn',
            Deductions.DeductionRate AS '@DeductionRate',

          CASE 
             WHEN SUM(LandingDetails.Quantity * LandingDetails.UnitPrice) - (SUM(LandingDetails.Quantity * LandingDetails.UnitPrice) * DeductionRate + WeeklyDeductionRate) > FromMinimumReturn 
             THEN SUM(LandingDetails.Quantity * LandingDetails.UnitPrice) * DeductionRate + WeeklyDeductionRate
             ELSE SUM(LandingDetails.Quantity * LandingDetails.UnitPrice) * DeductionRate 
          END AS '@TotalDeductions',

            (SELECT DISTINCT
                ld1.ProductId AS '@ProductId',
                FORMAT(AVG(ld1.UnitPrice), 'N2') AS '@Cost',
                FORMAT(SUM(ld1.Quantity), 'N2') AS '@Quantity'

            FROM LandingDetails ld1
            INNER JOIN dbo.LandingHeaders lh1
                ON ld1.LandingId = lh1.LandingId
            WHERE Posted = 0
            AND lh1.VesselOwner = LandingHeaders.VesselOwner
            GROUP BY ld1.ProductId
            FOR XML PATH ('Products'), TYPE)

        FROM dbo.LandingDetails
        INNER JOIN dbo.LandingHeaders
            ON LandingDetails.LandingId = LandingHeaders.LandingId
        INNER JOIN dbo.Vessels
            ON LandingHeaders.VesselId = Vessels.VesselId
        INNER JOIN dbo.Contacts
            ON Vessels.OwnerId = Contacts.ContactId
        INNER JOIN dbo.SocietyMemberships
            ON Contacts.SocietyId = SocietyMemberships.SocietyId
        INNER JOIN dbo.Deductions
            ON Vessels.DeductionId = Deductions.DeductionId
        WHERE LandingHeaders.Posted = 0
        AND LandingDate1 BETWEEN @startDate AND @endDate
        GROUP BY    ContactId,
                    LandingHeaders.VesselOwner,
                    SocietyMemberships.WeeklyDeductionRate,
                    SocietyMemberships.FromMinimumReturn,
                    Deductions.DeductionRate
        ORDER BY ContactId

        FOR XML PATH ('Owner'), TYPE)

    FOR XML PATH ('PurchaseOrders'), TYPE

END

A consulta provavelmente pode ser melhorada, mas sem definições de tabela e alguns dados de amostra, é um pouco difícil testá-la.

Confira este SQL Fiddle para uma versão ligeiramente ajustada que deve dar o mesmo resultado.