It means that something wrong with your project. I do not get such message when I use either 'Save as' or copy in the command window.

>I tried your suggestion to Save as. I don't know why you said that it is better than making a copy of the project files in command prompt, as I get the same results. Maybe I didn't clarify what I was trying to do initially. My goal is to make two project out of one. Initially both projects should point to exactly the same libraries, programs, etc. But then one project would be used as a test project for new modules. When I Save As initial project and then open the initial project I still get the prompt to make new home directory. It is not a big deal though.