When you started working on (or editing) a theme, did you copy the default directory and create your own, or have you just been editing/adding stuff in there? If so, you’ll want to make a copy of the theme directory (in both the app and skin directories) and rename it to something more appropriate.
The chnages I have done were removing the images that come with the default themes and fixing up all the email templates , removing all the magento stuff.
And the images and so on… I have downloaded the whole site just incase, I was just not looking forward re fixing everythign again LOL.. Thats all .........