[SOLVED] Warning messages received after updating to Atahualpa 3.5.3 from 3.4.9

I'm a new Atahualpa and Wordpress user in general, here is the site I am working on: www.kimberlygill.com.

I was making some edits in the wp-content/themes/atahualpa/functions.php file when I believe I made an error and added an extra "}" to the file. I tried to FTP the originally file back and then update my 3.4.9 to the current 3.5.3 in hopes that everything would be overwritten and I could continue as normal. However, now I am getting these warnings at the top of my Wordpress site:

Warning: include_once(/home/kimberagill/kimberlygill.com/wp-content/themes/atahualpa/functions/bfa_new_wp3_menus.php) [function.include-once]: failed to open stream: No such file or directory in /home/kimberagill/kimberlygill.com/wp-content/themes/atahualpa/functions.php on line 72

Warning: include_once() [function.include]: Failed opening '/home/kimberagill/kimberlygill.com/wp-content/themes/atahualpa/functions/bfa_new_wp3_menus.php' for inclusion (include_path='.:/usr/local/lib/php:/usr/local/php5/lib/pear') in /home/kimberagill/kimberlygill.com/wp-content/themes/atahualpa/functions.php on line 72

At this point, I am completely lost. Is there a way to save all of my content and restore Atahualpa 3.5.3? Thank you so much for your help.