Hi Pankaj,
I did a migration from 2.5 to 3 under a dev folder (ie www.site.com/dev). I then added the JA SImpli template, setup and configured everything.
When the site was finished, I zipped up the entire site, moved it to the root, and editted the configuration.php file. The problem is that logo disappeared on the live site, and when I tried to go to the Theme Customizer, it gave an error - it referenced the dev site.