Help with a logic inside WHERE or ORDER BY
I think you should be able to get what you want with ROW_NUMBER().  Please see the below example.

;with cte as (
Select tConc.Faturamento
     , tFat.TotalFatura
     , tCod.Sequencial
     , tCodDet.CdCodigoBarras
     , tCodDet.Linha
     , ValorRecebido
     , RN = ROW_NUMBER() OVER (PARTITION BY  tConc.Faturamento, tCod.Sequencial, tCodDet.CdCodigoBarras, ValorRecebido
                                ORDER BY tCodDet.Linha DESC, tCodDet.CdCodigoBarras DESC, tCod.Sequencial DESC)
  From Sistema.Conciliacao_Faturamento_x_Arrecadacao as tConc
 Inner Join Arquivo.CodigoBarras_Detalhe as tCodDet
    On tConc.CodigoBarras = tCodDet.CdCodigoBarras_Detalhe
 Inner Join Arquivo.CodigoBarras as tCod
    On tCodDet.CdCodigoBarras = tCod.CdCodigoBarras
 Inner Join Arquivo.Faturamento as tFat
    On tConc.Faturamento = tFat.CdFaturamento
 Where Faturamento In(Select Faturamento
                        From Sistema.Conciliacao_Faturamento_x_Arrecadacao
                       Group By Faturamento
                      Having Count(CodigoBarras) &gt; 01))
)
SELECT * FROM cte WHERE RN = 1


You may want to change or play with the PARTITION BY section as well as the ORDER BY to get what you want.  Basically, the PARTITION BY is what you want to be the business keys.  And I wasn't sure if it was just the Faturamento or Faturamento + Sequencial + ... or not.  Order by is if (given the same partition), what order should they appear in.