Incorrect :

SELECT * FROM tbFactura F.intFactura  NOT IN (SELECT intFacturaEnc FROM tbFacturaGlobalParametrosDet WHERE intEmpresa=@intEmpresa)

Correct:

SELECT * FROM tbFactura F.intFactura  NOT IN (SELECT ISNULL(intFacturaEnc, 0) FROM tbFacturaGlobalParametrosDet WHERE intEmpresa=@intEmpresa)

You need to use an ISNULL in the subquery to be sure that the results will be correct

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