Thanks for your suggestion marc. We would love to upgrade it directly to 6.5, but all this, automation and upgrade are client requirements which I personally cannot change. That was a nice piece of information though.

I am automating this AEM upgrade from 6.0 - 6.3 using Chef cookbook/recipes. For this I need to write two recipes. One which will automatically backup the repository content and other will upgrade the packages to 6.3. Any suggestions?