I`ve got the same problem. 
And Tools->Visual Micro->Reload Toolchain does not help. 

For sometime I worked in Arduino IDE so I can`t recognize the moment when compilation in VS has broken. Thank to topic starter - I found out the reason of such behaviour is the following: 
In Visual Micro documentation its recommenned to move your source code from libabry to project folder if you would like to debug libabry. Arduino IDE has no problem with it. But in VS you get a problem. You need to add source files to your project, only after that it works under Visual Micro.

The source file from the library. For instance, I have a Library StepperClass. It consist of two files: StepperClass.cpp and StepperClass.h. Usually its placed in Arduino\Lababry\StepperClass\. As other libraries StepperClass included into my projects ino file by #include "" or <>
And these libraries are not inlcuded into the VS solution (VS project - no reference).
VS has no problem with it - it works.

But if I would like to debug it, according to your documentation, I need to move library source files to project folder, Arduino\MyProject. 
If I do it, Arduino IDE still has no problem with, just open it with ino sketch automatically. 
But VS completely lost it. You have to add it into VS solution and after that only it works.

Hope this description is slightly more clear

Thanks to your question, only when I read it I guess what can be the reason