In answer to how I suspect that you may have inadvertently right clicked on the file in the project explorer - all to easy to do in VS.
How to make sure it doesn't happen in the future you have 2 options a) Don't use visual studio or b) Use a revision control system such as Mercurial and include the project file in those you are controlling - and do regular commits - you will be able to revert changes to the project file if needed and you should notice if it is in the changed file list when you are not expecting it to have changed.