--update dbo.MyDB_RowCnt

begin tran tt;

delete from Utility.dbo.MyDB_RowCnt

where flag ='OLD';

update Utility.dbo.MyDB_RowCnt

set flag ='OLD'

where flag ='NEW';

INSERT INTO Utility.dbo.MyDB_RowCnt

Select 'NEW' as flag

,QUOTENAME(SCHEMA_NAME(sOBJ.schema_id)) + '.' + QUOTENAME(sOBJ.name) AS [TableName]

, SUM(sPTN.Rows) AS [RowCount], GetDate() as Date

FROM ...

commit tran tt;

-- analyze OLD against NEW

P.S. If number of tables can possibly vary i'd better opt to FULL JOIN instead of LEAD /LAG.