Hmm. Finally completed Structure theme update for 5 Websites. It was horrible with those Visual Composer issues for 4.6.x. We got good support and successfully completed all WordPress core, Plugins and theme update.
Wp Rollback plugin was useful in rolling back plugins to earlier versions when we got conflicts with latest versions.Wp clone was another plugin which we found recently and very useful in replicating. Kudos to development team.