I love iTerm as a replacement for Terminal.app, but this morning after letting iTerm upgrade itself to “Build 0.9.5.0909”, all my settings, profiles and bookmarks were lost. I don’t know why, but that’s what happened. I pulled back the iTerm.plist from ~/Library/Preferences using Time Machine, but that didn’t seem to fix it. I also tried to restore iTerm.app using Time Machine, but there was something funky going on with TM, so I wasn’t able to.
In the end I just reset the preferences as best I could from memory and started recreating my bookmarks. You might want to wait to upgrade.