If you want rename .cpp/.h files in Visual Studio, just do it, they will become renamed on disk, not only in project.
If you want to remove files from Visual Studio project, you must do it outside of Visual Studio, manually, using Windows Explorer. Because if you remove files only in Visual Studio, they will not be deleted from disk and GenerateProjectFiles.bat will include that files to project again and again.
If you want add new files to Visual Studio project, best way to do this is to open your project in Unreal Editor and use Edit->AddCodeToProject.