--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.