In my case I had a solution with VB Web Forms project that referenced a C# UserControl. Both the VB project and the CS project had a Service Reference to the same service. The reference appeared under Service References in the VB project and under the Connected Services grouping in the CS (framework) project.
In order to update the service reference (ie, get the Reference.vb file to not be empty) in the VB web forms project, I needed to REMOVE THE CS PROJECT, then update the VB Service Reference, then add the CS project back into the solution.