SET TRANSACTION ISOLATION LEVEL READ UNCOMMITTED;

DROP TABLE IF EXISTS #tmp_Docs;

CREATE TABLE #tmp_Docs (
      [DealTransactID] NUMERIC(15, 0),
      [ResDebtID] NUMERIC(15, 0),
      [ResCredID] NUMERIC(15, 0),
      [Date] DATETIME,
      [Qty] MONEY,
      [Comment] VARCHAR(255),
      [ContractID] NUMERIC(15, 0)
);

DECLARE
       @DS DATETIME,
       @DE DATETIME,
       @BatchID NUMERIC(15, 0);

SET @DS = '20200401';
SET @DE = '20200501';
SET @BatchID = 10000003353;

INSERT INTO #tmp_Docs ([DealTransactID], [ResDebtID], [ResCredID], [Date], [Qty], [Comment])
  SELECT
        dt.[DealTransactID],
        dt.[ResourceID],
        dt.[ResourcePsvID],
        dt.[Date],
        dt.[Qty],
        dt.[Comment]
  FROM [dbo].[tDealTransact] dt WITH(FORCESEEK)
  WHERE dt.[TransactType] = 5
    AND dt.[Date] BETWEEN @DS AND @DE
    AND dt.[BatchID] = @BatchID
    AND dt.[Confirmed] = 1 --условия в вашем запросе нет, но наверняка плановые документы вам не нужны
    --AND dt.[InstrumentID] = 1558. --очень желательное условие: завязаться дополнительно на ФО в которой создается комиссия
    AND EXISTS (SELECT 1 FROM [dbo].[tResource] r WHERE r.[Brief] LIKE '70601%' AND r.[BalanceID] = 2140. AND r.[ResourceID] IN (dt.[ResourceID], dt.[ResourcePsvID]))
  OPTION (RECOMPILE);

UPDATE t
   SET [ContractID] = x.[ObjectID]
  FROM #tmp_Docs t
      CROSS APPLY (SELECT TOP(1)
                         cal.[ObjectID]
                   FROM [dbo].[tCrdAccountLink] cal
                       JOIN [dbo].[tTypeAccLink] tal ON tal.[TypeAccLinkID] = cal.[RuleID] AND tal.[Brief] = 'РАСЧЕТН' --тип связи уточнить
                   WHERE cal.[AccountID] = t.[ResDebtID]
                     AND cal.[Flags] = 2
                     AND cal.[ObjectID] IN (10000002061., 10000002062., 10000002063., 10000002370., 10000002372.)
                   ORDER BY cal.[OnDate] DESC
                  ) x;

UPDATE t
   SET [ContractID] = x.[ObjectID]
  FROM #tmp_Docs t
      CROSS APPLY (SELECT TOP(1)
                         cal.[ObjectID]
                   FROM [dbo].[tCrdAccountLink] cal
                       JOIN [dbo].[tTypeAccLink] tal ON tal.[TypeAccLinkID] = cal.[RuleID] AND tal.[Brief] = 'РАСЧЕТН' --тип связи уточнить
                   WHERE cal.[AccountID] = t.[ResCredID]
                     AND cal.[Flags] = 2
                     AND cal.[ObjectID] IN (10000002061., 10000002062., 10000002063., 10000002370., 10000002372.)
                   ORDER BY cal.[OnDate] DESC
                  ) x
 WHERE t.[ContractID] IS NULL;

WITH X AS (
    SELECT
          d.[DealTransactID],
          d.[ResDebtID],
          d.[ResCredID],
          FORMAT(d.[Date], 'yyyy.MM') AS [Period],
          d.[Qty],
          d.[Comment],
          c.[Number] AS [DealNumber]
    FROM #tmp_Docs d
        JOIN [dbo].[tResource] rd ON rd.[ResourceID] = d.[ResDebtID]
        JOIN [dbo].[tResource] rc ON rc.[ResourceID] = d.[ResCredID]
        JOIN [dbo].[tContract] c ON c.[ContractID] = d.[ContractID]
)
SELECT
     [Period],
     [ContractID],
     MAX([DealNumber]) AS [Dog],
     SUM([Qty]) AS [SumQty]
     --BLABLABLA CASE по поиску типа комиссии
     --BLABLABLA CASE по поиску текста по сути тоже можно предрасчетом подготовить что бы не писать безумных CASE
FROM X
GROUP BY [Period], [ContractID];