All customizations got re-set? Huh?

This morning I went to a page that I designed for a client and all the customizations look like they are gone. The custom fav.ico, header image, the widget layout, it's showing the default sample logo - crazy.

I have no idea how she would have done that. I am having her use the editor password so in theory, she should not have been able to mess something up (although she does have the admin password in her possession).

Right now I am on the phone with the host trying to see if we can restore to before the last time she did any updates but I don't know if this will fix it.

I guess what I failed to do was even though I downloaded the whole site via FTP before I handed it over, I didn't export the Ata theme options settings, so I don't think an FTP file is going to help me at all.

The other crazy thing is under ATO theme options
Configure Header Area

It says the default is this; Default: %pages %logo %bar1 %image %bar2
As far as I can tell all the settings were returned to the default. But in this box it has:

%logo %pages %cats
<!-- To remove the ad altogether, start removing here... -->
<div style="position:absolute;top:20px;right:20px;width :728px;height:90px;">
<!-- Put the ad code BELOW this (and remove the sample text if there is any) -->
%image
<!-- Put the ad code ABOVE this -->
</div>
<!-- End removing the ad here -->

Any idea what might have happened and what should I do in the future to prevent this? I have never, ever had a site get completely screwed up out of the blue unless there was an upgrade going on, and it doesn't look like there was an upgrade.