I just updated this site www.urbanbuiltllc.com to the latest version of Atahualpa using the automatic method within wordpress. I have always done this in the past, and have had to manually redo some customizations to rotating header images, favicon and customized footer content, and in the past this always worked fine.
This time, the favicon still does not appear even after re-putting the file, resaving the theme option favicon settings and clearing my browser cache.
More importantly, the footer for the whole site (not the post/page footer) does not appear. In the past, I always made some modifications to the footer_content manually in functions.php and had to redo those after updates, but this time I did not even see the generic wordpress/bfa footer after the update, it was just gone. My manual changes did not fix it.
From now on I guess I will use the manual update method, I've just never had difficulty using the auto method before so didn't anticipate these issues. Thanks for any help you can provide.