Microsoft has always been a polyglot corporation. Just because not all of their code is/will ever be managed code/.NET doesn't mean that Microsoft would abandon all of the good work that has gone into the .NET platform, its languages, managed code, the CLR platform...
.NET is still the "third pillar" of modern application development on Windows devices in the UWP and .NET is also more cross-platform than ever with big investments into Xamarin tooling (now a first party part of the Visual Studio team/Developer Division) and the open source, cross-platform .NET Core runtime.
With Windows 10, the native backend introduced on Windows 8.x was replaced by Visual C++'s backend, known as C2.
With C2, Microsoft is trying to make a kind of internal LLVM-like stack for their compilers, with clang, .NET and Visual C++.