The least painful method I've found is to use the Xcode Editor (free download from the Mac App Store) to reset iTerm 2's color-schemes to factory defaults as follows:
1. Quit iTerm
2. Open ~/Library/Preferences/com.googlecode.iterm2.plist with Xcode Editor (if it's not your default .plist editor, right click on the file in finder and choose "open with">"Xcode"
3. Delete the "Custom Color Presets" key
4. Re-import the color-schemes you want.
I do this whenever I do a `git pull` from the iTerm2 color-schemes repo. Not *too* painful.