Originally Posted by thesyndicate
To solve that upgrading that delete all your modifications, you can use the concept of Child Theme
for your site.
It involves some learning though and the documentation in AppThemes are available for only Action Hooks. There isn't basic introduction on child theme for us to do that easily.
I have started to add a child theme to my new site now and the basic work is working and I am still learning on how to add more features to the child theme.
You can learn about Child Theme here:
Child Theme WordPress Codex
A WordPress child theme is a theme that inherits the functionality of another theme, called the parent theme, and allows you to modify, or add to, the functionality of that parent theme. This article shows how to create a basic child theme and explains what you can do with it.
Making a child theme is very simple. Create a directory, put a properly formatted style.css file in it, and you have a child theme! With a little understanding of HTML and CSS, you can make that very basic child theme modify the styling and layout of a parent theme to any extent without editing the files of the parent theme itself. That way, when the parent theme is updated, your modifications are preserved.
For this reason, child themes are the recommended way of making modifications to a theme.
Basic Introduction to Child Theme
Basic Introduction to Child Theme on SlideShare
How to Modify WordPress Themes the Smart Way - four-part series on child themes
Learn By Examples
How to: Create a Child Theme Based on Twenty Eleven
Introducing Thirty Ten, my guide to creating a Twenty Ten Child Theme