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 not available for us to do that easily.
You can learn about Child Theme here:
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
http://www.firsttracksmarketing.com/wp-content/uploads/2011/06/WordPressChildThemePresentationHandout.pdf
Basic Introduction to Child Theme on SlideShare
http://www.slideshare.net/rfair404/wordpress-child-themes
How to Modify WordPress Themes the Smart Way – four-part series on child themes
http://themeshaper.com/modify-wordpress-themes/
Learn By Examples
How to: Create a Child Theme Based on Twenty Eleven
http://theme.fm/2011/07/how-to-create-a-child-theme-based-on-twenty-eleven-791/
Introducing Thirty Ten, my guide to creating a Twenty Ten Child Theme
http://aaron.jorb.in/blog/2010/04/introducing-thirty-ten/#.TwvBZ2_9N2A
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