A loop like this will do the trick.  You can keep changing the WHERE clause to do different batches
CREATE TABLE #Staging (
  ID      INT NOT NULL
, PTL_EndDate   VARCHAR(20)
, Clean_PTL_EndDate DATE
);

INSERT INTO #Staging (ID, PTL_EndDate)
VALUES ( 117915, '27.01.2014' )
  , ( 117916, '15.27.2014' )
  , ( 117916, '01.27.14' )
  , ( 117917, '2014.01.27' )
  , ( 118301, '27.01.2014' )
  , ( 118302, '01.27.2014' );

DECLARE @BatchSize INT = 1; -- Start with a big number, and keep making it smaller

BEGIN TRY
WHILE EXISTS (SELECT 1 FROM #Staging
      WHERE Clean_PTL_EndDate IS NULL
      AND (PTL_EndDate LIKE '[0-3][0-9].[0-1][0-9].[0-9][0-9][0-9][0-9]'
       OR PTL_EndDate LIKE '[0-1][0-9].[0-3][0-9].[0-9][0-9][0-9][0-9]')
     )
BEGIN
  WITH cteBatch AS (
  SELECT TOP (@BatchSize)
    ID
   , PTL_EndDate
   , Clean_PTL_EndDate
   , YearPart = PARSENAME(PTL_EndDate, 1)
   , MonthPart = CASE WHEN PARSENAME(PTL_EndDate, 2) > 12 THEN PARSENAME(PTL_EndDate, 3) ELSE PARSENAME(PTL_EndDate, 2) END
   , DayPart = CASE WHEN PARSENAME(PTL_EndDate, 2) > 12 THEN PARSENAME(PTL_EndDate, 2) ELSE PARSENAME(PTL_EndDate, 3) END
  FROM #Staging
  WHERE Clean_PTL_EndDate IS NULL
   AND (PTL_EndDate LIKE '[0-3][0-9].[0-1][0-9].[0-9][0-9][0-9][0-9]'
    OR PTL_EndDate LIKE '[0-1][0-9].[0-3][0-9].[0-9][0-9][0-9][0-9]')
  ORDER BY ID
  )
  UPDATE cteBatch
  SET Clean_PTL_EndDate = CONVERT(date, DayPart + '.' + MonthPart + '.' + YearPart, 104);

  WAITFOR DELAY '00:00:00.100'; -- Pause for 100ms
END;
END TRY
BEGIN CATCH
-- Somewhere in this batch you should find your bad apple.
-- If this returns no data, then the specific pattern has been taken care of
SELECT TOP (@BatchSize) *
FROM #Staging
WHERE Clean_PTL_EndDate IS NULL
AND (PTL_EndDate LIKE '[0-3][0-9].[0-1][0-9].[0-9][0-9][0-9][0-9]'
  OR PTL_EndDate LIKE '[0-1][0-9].[0-3][0-9].[0-9][0-9][0-9][0-9]')
ORDER BY ID;
END CATCH