I realise I don't need to edit the makefile I just need to edit the files it reads from as I have not worked with Arduino and Teensyduino for a while and it is somewhat of a mess. I have just edited my preferences file to point to the correct location for my shared libs and am now trying VisualTeensy again but it crashes:
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Object reference not set to an instance of an object.
System.NullReferenceException: Object reference not set to an instance of an object.
at vtCore.Makefile_Make.generate(IProject project, LibManager libManager, SetupData setup)
at ViewModel.ProjectTabVM..ctor(IProject project, LibManager libManager, SetupData setup) in U:\HAK\Arduino\Github\VisualTeensy\VisualTeensy\ViewModel\ProjectTab\ProjectTabVM.cs:line 292
at ViewModel.MainVM..ctor(IProject project, LibManager libManager, SetupData setup) in U:\HAK\Arduino\Github\VisualTeensy\VisualTeensy\ViewModel\MainWin\MainVM.cs:line 61
at VisualTeensy.App.OnStartup(StartupEventArgs e) in U:\HAK\Arduino\Github\VisualTeensy\VisualTeensy\App.xaml.cs:line 180
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OK
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... I have just loaded the source in VS and was going to have a look what is going on.