I just updated from 3.7.12 to 3.7.13 thru my updates dashboard and all my headers and footers in my multi-site installation are gone. I've looked at my Atahualpa options, but everything seems to be fine there.
I would try to roll back to 3.7.12 but can't find a download link for it anywhere.
Any ideas? You can see one of my sites here- http://debslosingit.com/