This happened to me today, And thank the gods I randomly had a backup of the custom theme folder. I had updated some function calls to make it load a bit faster, and I lost those when I decided to upgrade to the latest version of WordPress 2.8.1.
I had manually installed WordPress 2.8 (which I thought was the latest version that I downloaded), but was not. After that upgrade the site worked perfectly and I wasn’t thinking and I clicked on Upgrade to 2.8.1. Whoops, lost my themes folder.
But always backup when upgrading, It will save you a lot of headaches in the future. And just always backup randomly. You never know, and it doesn’t hurt.
