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Incrustar una declaración de caso sql en una consulta sql que usa FOR XML

Creo que insertar la expresión de caso original en el lugar correcto debería funcionar. Prueba esto:

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

La consulta probablemente se puede mejorar, pero sin definiciones de tablas y algunos datos de muestra, es un poco difícil probarla.

Mira este SQL Fiddle para una versión ligeramente modificada que debería dar el mismo resultado.