Lost customization with WordPress update

Hey there! My company uses WordPress for our blog and the free Twenty Ten theme.

Recently, we upgraded to WordPress 3.8.1 and some of the custom design work a former employee put in has disappeared.

Also, Google Analytics code has also disappeared from the source code.

We use BackUp buddy but have posted several blogs since updating to 3.8.1.

Is it typical to lose custom work when upgrading to a different version of WordPress?

Here is the blog:

http://www.cushingco.com/blog

We have the latest version of the theme running and all our plug ins are the latest version.

Any assistance or direction is appreciated.