How to exclude a ino/pde file from Arduino projects
One possible approach is to guard the body of that sketch with an #ifdef ... #endif pair, and use Visual Micro's  “Project Properties” to define (or not) a preprocessor symbol.  [If the .ino or .pde in question is used as a #include file, you would instead guard all the #include instances.]

Refer to the “Project Defines” page at visualmicro.com for how to define a preprocessor symbol and its value. [Via: Tools > Options > Visual Micro > Compiler > Show Build Properties]  Also see  How do I add additional compiler switches in Visual Studio.

If necessary, you can use other tests besides #ifdef to control compilation.  The first link above shows the following example.

#if USBPORT &gt; 3
....your code here....
#endif