In copyright removal document ( log into sign up page via http://www.joomlart.com/member/signup.php >> go to Your payment history group at the bottom >> Focus on PDF Copyright Removal column and get that file), we provide instruction to remove it in the proper way.
You should copy that default.php file in t3 plugin folder and copy it to /templates/ja_template_name/html/mod_footer directory and make your own change there. This override will allow you to customize without fear of losing your work when updates of JAT3 plugin appears.
However, the best way is that you should take a BACKUP of file you change before upgrading 🙂