Sounds like something moved or was deleted. Can you locate your project folder on your computer's disk? If so, you can use the green button labeled "open an intel xdk project" at the lower left of the Projects tab in the XDK.
Actually this problem I recovered 3 weeks ago by creating a new project and transfer my files into it.
Now it just happened again .. and there is no reference or guidelines how to find a solution for this problem.
I think It was stupidity to depend on such beta program as intel xdk, unfortunately it is time to deploy to another stable solution.