A customer was asking about this issue when he can see a certain file in source control explorer and locally on disk but it doesn’t show in Solution Explorer. What happened was the file was removed from the project file. If you're using C#, the project file is a .csproj file that you can open in a text editor to view its XML content, for each included file there will be a node like this:

    <Content Include="FileName.ext">

You can view the history of the project file and see who changed it and compare the versions to see what was changed. You may add a node like that with the file path in the Include attribute to include the file back in the project.