after upgrade, all images missing

Simple question: has anyone else had a strange upgrade experience after upgrading Atahualpa? In a nutshell, my images were overwritten/erased and many (but not all) of my Atahualpa settings are messed up.

I'm completely stunned to have found that upon upgrading, all of my site's folders and files in the Atahualpa theme folder were erased and replaced with new defaults. That is, all of my header images and my logo were missing. I don't mean that they weren't displaying correctly. I mean they are *nowhere to be found* on my server!

I've spent hours trying the tips posted in other threads about upgrade problems (here, in other WP forums about upgrading Atajualpa, and on the web in general) to figure out what happened. Now I'm just trying to rebuild the entire site.

I don't know what's going on, but it's terribly disappointing. (To say the least.) As a one-person business who already has busy days, the last thing I needed today was a total theme rebuild.

I'm just dying to know if anyone else here has experienced something similar?

If so, what the heck is the most efficient way to rebuild a large site? My backup didn't work because I get errors saying the folders already exist. Hrmph.

Thanks for any info that any of you can provide.