Dfyjkt

I have a SQL Server file with 50,000 update queries like this:

UPDATE [dbo].[TABLE1] SET [COLUMN2] = 'abc123' WHERE [Id] = 100;
UPDATE [dbo].[TABLE1] SET [COLUMN2] = 'def456' WHERE [Id] = 101;
UPDATE [dbo].[TABLE1] SET [COLUMN2] = 'ghi789' WHERE [Id] = 205;
UPDATE [dbo].[TABLE1] SET [COLUMN2] = 'jkl012' WHERE [Id] = 216;
UPDATE [dbo].[TABLE1] SET [COLUMN2] = 'mno345' WHERE [Id] = 350;

I don't want to run this file and execute all 50,000 queries at once.
What is the best way to do this by executing 1000 queries at a time, and when these are done move on to the next 1000 until all are executed?
Also If I get an error how would I do a rollback?

You should create a temporary table with the values. You can then use this for the update. Absent that, you can create a derived table in the query:

with t as (
 select v.*
 from (values (100, 'abc123'),
 (200, 'def456'),
 . . .
 ) v(id, column2)
 )
update t1
 set column2 = t.column2
 from dbo.table1 t1 join
 t
 on t1.id = t.id;

use CASE WHEN statement

UPDATE [dbo].[TABLE1] 
SET [COLUMN2] = CASE [Id]
 WHEN 100 THEN 'abc123'
 WHEN 101 THEN 'def456'
 WHEN 205 THEN 'ghi789'
 WHEN 216 THEN 'jkl012'
 WHEN 350 THEN 'mno345'
 END
WHERE [Id] IN ( 100 , 101, 205, 216, 350 )

You can try to use UNION ALL create a result set and write row number for it then do UPDATE .... JOIN.

What is the best way to do this by executing 1000 queries at a time?

If you want to update date for 1000 batch you can try to use loop (while) with variables to control.

DECLARE @fromNum int = 1;
DECLARE @toNum int = 1000;
DECLARE @totalRowNum int;

;with cte as (
 SELECT 'abc123' COLUMN2,100 ID
 UNION ALL
 SELECT 'def456' ,101 
 UNION ALL 
 SELECT 'ghi789' ,205 
 UNION ALL 
 SELECT 'jkl012' ,216 
 UNION ALL 
 SELECT 'mno345' ,350 
), cteRowNum as(
 SELECT *,ROW_NUMBER() OVER(ORDER BY (SELECT ID)) rn
 FROM cte
)
SELECT *
INTO #Temp
FROM cteRowNum

SELECT @totalRowNum = MAX(rn) 
FROM #Temp

While(@toNum < @totalRowNum)
BEGIN
 BEGIN TRY
 BEGIN TRAN
 update t1
 set t1.COLUMN2 = t2.COLUMN2
 from TABLE1 t1 join #Temp t2 on t1.id = t2.ID 
 where t2.rn between @fromNum and @toNum
 COMMIT TRAN
 END TRY
 BEGIN CATCH
 　ROLLBACK TRAN
 　SELECT ERROR_NUMBER() AS ErrorNumber,ERROR_SEVERITY() AS ErrorSeverity,ERROR_STATE() AS ErrorState,ERROR_PROCEDURE() AS ErrorProcedure,ERROR_LINE() AS ErrorLine,ERROR_MESSAGE() AS ErrorMessage
 END CATCH

 SET @fromNum = @toNum
 SET @toNum = @toNum + 1000
END

IF OBJECT_ID('dbo.Scores', 'U') IS NOT NULL 
DROP TABLE #Temp