If you are looking for the file in VS, it is likely that the file still exists in your directory, but is simply no longer referenced in the project (Since VS will only show you files in your project). If the file was renamed, that is likely why you can no longer find it in Visual Studio. I would check the actually directory where the file used to exist.
If it is not there, you can retrieve the old file from the repository by clicking on the containing directory and reverting to a previous revision that contains the file (file deletes are operations on the directory).
Your local copy of the file should not be deleted if there are modifications. This type of thing is annoying, but hopefully doesn't happen very often (how often do you rename files?). Of course, this is also exactly why you should update before committing. In this case, you need to manually merge the changes you made to the old file into the new file and make sure that it all still compiles.