If you're using the Sourcegear Vault client plugin for Visual Studio and use the feature "work offline", you have probably encountered this problem. If you added file while being offline, the added files won't be added to Vault after you "Go Online". The vault client thus silently corrupts your codebase.
I learned the hard way that i have to open each and every folder where i could possibly have added new files, to manually add them to vault after going online. But lately I discovered a good workaround. You can right-click on the project file, and choose "Add to vault" on the project root. All files that have not been added yet, will be added by that action.