Got it... Batch file calls below code and call it the day. Thanks!

import com.crystaldecisions.sdk.occa.security.ILogonTokenMgr;
import com.crystaldecisions.sdk.exception.SDKException;
import com.crystaldecisions.sdk.framework.*;
import com.crystaldecisions.sdk.occa.infostore.*;
import com.crystaldecisions.sdk.plugin.desktop.samlserviceprovider.ISAMLServiceProvider;
import java.util.Properties;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;


public class createSamlHanaCert{
	public static void main (String[] args) throws SDKException, IOException {


		String strUserName = args[0];
	    String strPassword = args[1];
	    String strCms = args[2];
	    String strAuthType = args[3];	    
	    String strHost = args[4];
	    String strHanaPort = args[5];
	    String strPID = args[6];
	    String strSpID = args[7];
	    String strSavePath = args[8];	
		
	    System.out.println("Login CMS "+strCms);  	    
	    String strToken = "";
	    new Properties();
	    IEnterpriseSession boEnterpriseSession = null;
	    
	    try{	
			IInfoStore boInfoStore;
			IInfoObjects boInfoObjects;
			IInfoObject boObject;
			boEnterpriseSession = CrystalEnterprise.getSessionMgr().logon(strUserName, strPassword, strCms, strAuthType);
		    ILogonTokenMgr tokenMgr = boEnterpriseSession.getLogonTokenMgr();
	    	strToken = tokenMgr.getDefaultToken();			    	    
		    System.out.println("Login Completed - Token = "+strToken);
		    boInfoStore = (IInfoStore) boEnterpriseSession.getService("", "InfoStore");


		    boInfoObjects = boInfoStore.query("Select * from CI_SYSTEMOBJECTS where SI_PROGID='CrystalEnterprise.SAMLServiceProvider'");


		    if ( boInfoObjects.size() == 0 ) {
		        System.out.println("No HANA connection found") ;
		    } 
		    
		    OutputStream outputStream = new FileOutputStream (strSavePath);
		    Writer outputStreamWriter = new OutputStreamWriter (outputStream);
		    
		    // loop through the HANA connections     
		    for( int i=0; i < boInfoObjects.size(); i++ ) {
		         boObject = (IInfoObject) boInfoObjects.get(i) ;
				 boObject.getParentID();
				 ISAMLServiceProvider sp = (ISAMLServiceProvider) boObject;
				 
				 //Set Host/Port/SAML/SpID
				 sp.setSpHost(strHost);
				 sp.setSpPort(Integer.parseInt(strHanaPort));
				 sp.setIdPID(strPID);					 
				 sp.setSpID(strSpID);
				 
				 //Get Info
		         String connectionName = sp.getTitle();
		         String connectionCUID = sp.properties().get("SI_CUID").toString() ;
		         String	spHost = sp.getSpHost();
				 int spPort = sp.getSpPort();
				 String spIdPID = sp.getIdPID();
				 sp.getSiteUrl();
				 String	spSpID = sp.getSpID();
				 sp.getSpAcsUrl();
				 sp.getSpSloUrl();
				 String	spIdPBase64Certificate = sp.getIdPBase64Certificate() ;
		      
				 System.out.println( "------" );				 
				 System.out.println( "Old Certificate - " + spIdPBase64Certificate);
				 System.out.println( "------" );	
				 			 
				 String	spGenerateIdPBase64Certificate = sp.generateIdPBase64Certificate();
				 System.out.println( "New Certificate - " + spGenerateIdPBase64Certificate);
				 boInfoStore.commit(boInfoObjects);
				 
				 outputStreamWriter.write(spGenerateIdPBase64Certificate);
				 outputStreamWriter.close();
				 
				 System.out.println( "------" );
				 System.out.println( "connectionName - " + connectionName);
				 System.out.println( "connectionCUID - " + connectionCUID);
				 System.out.println( "spHost - " + spHost);
				 System.out.println( "spPort - " + spPort);
				 System.out.println( "spIdPID - " + spIdPID);
				 System.out.println( "spSpID - " + spSpID);
				 System.out.println( "------" );
		      }
		        
		}  catch(Exception e){
	    	System.out.println(new java.util.Date()+": error occured: "+e);
	    } 
	    finally { 	    	
	    	System.out.println("\n Releaseing BO Session!");  	    
	    	boEnterpriseSession.logoff();	    	
	    }	
	}
}