Upgraded Unity wipes out my source tree

I have a foder structure something like:

- MyProj
   |- Unity-iPhone.xcode
   |- All my unrelated but very important source folders and files.
   |- Unity Project
      |- Assets
      |- Scripts
      |-etc

So when I build an iOS build within Unity it has been building into MyProj, appending the xcode data.

This has been working great until I upgraded to 3.1.0f3. Now when I build it deletes the entire MyProj folder first and then tries to build. Obviously this fails completely because it just deleted itself and a bunch of unrelated but very important code.

So I just lost the whole days work :frowning:

So if you go through the build dialog you get a nice warning. It shows you a replace option but no append option. I can live with that.

If you hit the Apple+B then it just wipes it for you with no warning.