So I spent six hours this morning working on my first theme - probably edited 30 or 40 elements. I save and go to lunch. I come back and start back at it, edit one element, save and I lost everything but that one element. It didn't seem to ever ask me which theme I was editing and Sonar wasn't open at the time - obviously I started editing mercury while thinking I was editing my new theme so when I saved under the new theme name I lost it all. Seems like it was too easy to make this mistake, grrrrrr...

YEP!  i made this mistake while working on it too.   But if you think about it, it's our fault.   Think of it as any application, like Microsoft Word.  You open up word, you HAVE to open your document before modifying it.   

For some reason though, I fell for this too!  Must be something in the way it "feels" hehe.
 
Maybe a quick dialog upon opening like Word does - "New Theme Based On" or "Edit Existing Theme" should pop up first thing!