Update unpivoted table with one to many relation
DECLARE @ExistentData 
TABLE (ID INT IDENTITY(1000,1), [Row] INT, [Col] INT, Val NVARCHAR(50));

INSERT INTO @ExistentData([Row], [Col], Val)
VALUES 
(1,10,'Value 1'),
(1,11,'Value 2'),
(1,12,'Value 3.1'),
(1,12,'Value 3.2')
select * from @ExistentData    

DECLARE @NewDataToUpdateExistent TABLE ([Row] int, [Col] int, Val nvarchar(50));
INSERT INTO @NewDataToUpdateExistent([Row], [Col], Val)
VALUES 
(1,10,'Updated Value 1'),
/*(1,11,'Deleted Value 2'),*/
(1,12,'Updated Value 3.1'),
(1,12,'Updated 3.2'),
(1,12,'New Value 3.3')
select * from @NewDataToUpdateExistent


With ROW_NUMBER you do the trick

DECLARE @A TABLE (ID INT, [Row] INT, [Col] INT, Val NVARCHAR(50), [RowNumb] INT);
INSERT INTO @A (ID, [Row], [Col], Val, RowNumb)
SELECT A.ID, A.[Row], A.Col, A.Val,
ROW_NUMBER() OVER 
    (PARTITION BY A.[Row], A.[Col] ORDER BY A.[Row], A.[Col] DESC) AS RowNumb
FROM @ExistentData A
;

DECLARE @B TABLE ([Row] INT, [Col] INT, Val NVARCHAR(50), [RowNumb] INT);
INSERT INTO @B ([Row], [Col], Val, RowNumb)
SELECT B.[Row], B.Col, B.Val,
ROW_NUMBER() OVER 
    (PARTITION BY B.[Row], B.[Col] ORDER BY B.[Row], B.[Col] DESC) AS RowNumb
FROM @NewDataToUpdateExistent B
;


Now just joining tables in the following way you get the expected result

--Delete
DELETE ed
FROM @A a
LEFT OUTER JOIN @B b 
    ON  a.[Row] = b.[Row] AND a.[Col] = b.[Col] 
    AND a.[RowNumb] = b.[RowNumb]
INNER JOIN @ExistentData ed ON a.ID = ed.ID
WHERE b.[Row] IS NULL

--Update
UPDATE ed
SET ed.Val = B.Val
FROM @A a
INNER JOIN @B b 
    ON  a.[Row] = b.[Row] AND a.[Col] = b.[Col] 
    AND a.[RowNumb] = b.[RowNumb]
INNER JOIN @ExistentData ed ON a.ID = ed.ID

--INSERT
INSERT INTO @ExistentData([Row], [Col], Val)
SELECT b.[Row], b.[Col], b.Val
FROM @B b
LEFT OUTER JOIN @A a 
    ON a.[Row] = b.[Row] AND a.[Col] = b.[Col] 
    AND a.[RowNumb] = b.[RowNumb]
WHERE A.[Row] IS NULL



  SELECT * FROM @ExistentData
      ORDER BY id


ID          Row         Col         Val
----------- ----------- ----------- --------------------------------------------------
1000        1           10          Updated Value 1
1002        1           12          Updated Value 3.1
1003        1           12          Updated Value 3.2
1004        1           12          New Value 3.3