Stored Procedure, to create missing primary keys at target database by comparing both source and target databases.

SYNC_CreatePrimaryKeys.sql

--DROP IF ALREADY CREATED
IF EXISTS ( SELECT  1
            FROM    SYS.procedures
            WHERE   NAME = 'SYNC_CreatePrimaryKeys' ) 
    DROP PROC SYNC_CreatePrimaryKeys
GO

--CREATE PROCEDURE
SET ANSI_NULLS ON
GO
SET QUOTED_IDENTIFIER ON
GO
/*
Stored Procedure, to create missing primary keys at target database by comparing both source and target databases. 

EXEC [dbo].[SYNC_CreatePrimaryKeys] 'AdventureWork_StableVersion','AventureWork_Target'

*/
CREATE PROCEDURE [dbo].[SYNC_CreatePrimaryKeys]
    (
      @SyncFromDB VARCHAR(200), --Source database name
      @SyncToDB VARCHAR(200) --Target database name
    )
AS 
    BEGIN



        CREATE TABLE #AlterStatements ( TSQLStmt VARCHAR(MAX) )
			  EXEC('
					INSERT INTO #AlterStatements (TSQLStmt)
					SELECT '' IF NOT EXISTS(SELECT 1 FROM '+@SyncToDB+'.SYS.OBJECTS WHERE NAME  = ''''''+Constraint_name+'''''')  ALTER TABLE ['+@SyncToDB+'].[''+table_schema+''].[''+Table_name+''] ADD CONSTRAINT ''+Constraint_name+'' PRIMARY KEY CLUSTERED 
						(''+
						REVERSE(CASE WHEN LEFT(LTRIM(REVERSE(KEYCOLS)),1)='',''THEN SUBSTRING(REVERSE(KEYCOLS),CHARINDEX('','',REVERSE(KEYCOLS),1)+1,LEN(REVERSE(KEYCOLS))) ELSE REVERSE(KEYCOLS) END)
						+
						'') 
					ELSE 
				
					 ALTER TABLE ['+@SyncToDB+'].[''+table_schema+''].[''+Table_name+''] ADD CONSTRAINT ''+Constraint_name+''_1 PRIMARY KEY CLUSTERED 
					(''+
					REVERSE(CASE WHEN LEFT(LTRIM(REVERSE(KEYCOLS)),1)='',''THEN SUBSTRING(REVERSE(KEYCOLS),CHARINDEX('','',REVERSE(KEYCOLS),1)+1,LEN(REVERSE(KEYCOLS))) ELSE REVERSE(KEYCOLS) END)
					+
					'') ''
					FROM(	
					SELECT TC.TABLE_SCHEMA,TC.TABLE_NAME,TC.CONSTRAINT_NAME	,SUBSTRING(list,1,LEN(list)-1) AS kEYCOLS
					FROM  '+@SyncFromDB+'..sysobjects so 
						  INNER JOIN '+@SyncFromDB+'.information_schema.table_constraints tc ON tc.Table_name = so.Name AND tc.Constraint_Type  = ''PRIMARY KEY''
					CROSS APPLY
						(
						 SELECT ''[''+ Column_Name + ''], ''''''
						 FROM   '+@SyncFromDB+'.information_schema.key_column_usage kcu
						 WHERE  kcu.Constraint_Name = tc.Constraint_Name
						 ORDER BY
							ORDINAL_POSITION
						 FOR XML PATH('''')
						 ) j (list)
					 )MASTERDB
					WHERE NOT EXISTS
									 (
									  SELECT * FROM
										(	
										 SELECT TC.TABLE_SCHEMA,TC.TABLE_NAME,TC.CONSTRAINT_NAME	,SUBSTRING(list,1,LEN(list)-1) AS kEYCOLS
										 FROM  '+@SyncToDB+'..sysobjects so 
										 INNER JOIN '+@SyncToDB+'.information_schema.table_constraints tc ON tc.Table_name = so.Name AND tc.Constraint_Type  = ''PRIMARY KEY''
										 CROSS APPLY
											(
											 SELECT ''['' + Column_Name + ''], ''''''
											 FROM   '+@SyncToDB+'.information_schema.key_column_usage kcu
											 WHERE  kcu.Constraint_Name = tc.Constraint_Name
											 ORDER BY	ORDINAL_POSITION
											 FOR XML PATH('''')
											 ) j (list)
										 )SLAVERDB
										 WHERE SLAVERDB.TABLE_NAME=MASTERDB.TABLE_NAME
											   AND SLAVERDB.TABLE_SCHEMA=MASTERDB.TABLE_SCHEMA
											   AND SLAVERDB.kEYCOLS=MASTERDB.kEYCOLS			 
									 )
			 
			     
			     
			  ')  
  
			----CURSOR TO EXECUTE/PRINT EACH STATEMENT SEPARATELY-----
        DECLARE MY_CURSOR CURSOR READ_ONLY
            FOR SELECT  TSQLStmt
                FROM    #AlterStatements
   
        OPEN My_Cursor 
        DECLARE @ObjectName VARCHAR(MAX),
            @SQLstmt VARCHAR(MAX)

        Fetch NEXT FROM MY_Cursor INTO @ObjectName
        While ( @@FETCH_STATUS <> -1 )
            BEGIN

                SELECT  @SQLstmt = REPLACE(@ObjectName, '''[', ' [')
                EXEC ( @SQLstmt
                    )
			--	PRINT (@SQLstmt)
                FETCH NEXT FROM MY_CURSOR INTO @ObjectName
            END
        CLOSE MY_CURSOR
        DEALLOCATE MY_CURSOR
   -----

        DROP TABLE #AlterStatements
  
    END