I'm a little confused, do you have the retail version or Steam version of Amnesia?
If retail:
Simply reinstall Amnesia via its disc. If you're worried, simply point the installer directory to another folder other than Amnesia - The Dark Descent. Perhaps just a generic folder called Amnesia
If steam:
You can do this one of two ways I believe:
1. Right click Amnesia - The Dark Descent in Steam and go to Properties. Once there, navigate to Local Files and click Verify Integrity of Game Cache. That should replace any files which are missing.
2. If the previous method did not work, simply click that option above it - Delete Local Game Content. Then once that process is complete, go to Amnesia's steam page while logged in as yourself and redownload and reinstall.