I am using 5.0-716 and working with external dependencies.
Once I reference the dlls via Ctrl+E, it is all okay as it should be. But the moment I reference any other VL.Nuget from the dependency menu; all the external dlls will be lost!
My two cents : also happens on latest preview (737) if referencing a dll, but not if you reference a csproj instead. But maybe you’re using some external dll, so referencing a csproj might not apply here.