I made changes to my site's code in order to add epub and mobi file upload functionality as well as to fix consequent issues with Mac users. These changes affected the functions.php and, at the server end, the htaccess file. Previously, I also added Google Analytics code. In the past, when I upgraded to the next WP version I don't recall having any issues with the additional code being erased or overwritten, but I'd like to make sure before I do so now to 3.3. Does anyone know if updating will affect the changes I made?