Are you in this situation ?
Problems with .NET SDK SOE templates at 10.2 in Visual Studio 2012 prevent the .soe file from being generated.
The cause of this bug and the issue you are having are the same.
The workaround would be :
Edit the project file *.csproj:
Near the bottom of the XML you will see an Import element. For both Project and Condition, update the path from Server.targets to Server.11.targets.