What is the best way to make a project move from one folder to another in web .?

Hi currently we have a website and it contain some files in server . We developed second version and third version for the website in version2 , version3 folders . So now we are accessing the version2 through http://ift.tt/2oGsjrR .

Most of the files are html ,css, js& some php files too.

We want to make version2 live . So please sugest better method for moving the project without loasing any files and seo .

What we are planing is delete all files in in server and copy files from version2 , and put version3 same as before . It is a good idea ? Please suggest better methods .

Also we are thinking about down time of the website during migration and Seo is too much important . Please sugest