Stick with auto. In that case, as long as you still use the same app ID, you should be fine. I have deleted my C2 export folder before (with XDK project files in it) and created a new XDK project with the same info, and it was fine.
edit: to use manual, un-check the 'Signed' box, but only if you want more work (and you'll have to ask Intel for the keystore)