I was right in my analysis.It was the problem CCS or eclipse .It was just looking into C drive instead of the project workspace.
when i put the files in C drive it not only find the files but all the build files and object was also in C drive.
Then i found real issues was in registry.
It was really tough .
I am not sure CCS or Eclipse who is responsible for it .
but I have a recommendation that when it build and it cannot go to that directory it should throw error to show path which it is looking for.
Since we don't know what causes registry to go corrupt it will be better if anyone else face this issue they will at least know what path it is trying to take.
second recommendation is if how did CCS write Obj file or out outside the given path.It should never Happen.
Please forward this request to design team to check if they cannot open directory mentioned in the project path setting what they do.
Please review that path of error.