Hello,

I just updated VM to the latest version 1.1609.04 (I checked it in the VM options) within Visual Studio 2015 V14.0.25425.01 Update 3.
Arduino IDE is 1.6.11.
Right after that my project complained with the error above.

I set compiling to verbose, cleaned the build and then recompiled. Same error.

The last section of the details says:

Compiling debug version of 'BatteryCharger' for 'Arduino/Genuino Mega w/ ATmega2560 (Mega 2560)'
Build folder: mega2560
Additional Defines: VM_DEBUG;VM_DEBUG_ENABLE 1;VM_DEBUG_BANDWIDTH_THROTTLE_MS 50;VM_DEBUGGER_TYPE_HARDWARESERIAL 0;VM_DEBUGGER_TYPE_SOFTWARESERIAL 1;VM_DEBUGGER_TYPE_FASTSERIAL 2;VM_DEBUGGER_TYPE_USB 3;VM_DEBUGGER_TYPE_TEENSY 4;VM_DEBUGGER_TYPE_UART 5;VM_DEBUGGER_TYPE_USART 6;VM_DEBUGGER_TYPE_USBSERIAL 7;VM_DEBUGGER_TYPE_TTYUART 8;VM_DEBUGGER_TYPE_NET_CONSOLE 9;VM_DEBUGGER_TYPE_Uart 10;VM_DEBUGGER_TYPE_COSA 11;VM_DEBUGGER_TYPE_CDCSerialClass 12;VM_DEBUGGER_TYPE_HARDWARESERIAL1 13;VM_DEBUGGER_TYPE_HARDWARESERIAL2 14;VM_DEBUGGER_TYPE_HARDWARESERIAL3 15;VM_DEBUGGER_TYPE VM_DEBUGGER_TYPE_HARDWARESERIAL;VM_DEBUG_BREAKPAUSE;
Architecture Tools: {runtime.tools.avr-gcc.path}/bin/
Sketchbook: file:\\\H:\Development\Arduino
Sketch Include Paths
Core Include Paths
Include Path 'D:\Program Files (x86)\Arduino\hardware\arduino\avr\cores\arduino'
Include Path 'D:\Program Files (x86)\Arduino\hardware\arduino\avr\variants\mega'
"{runtime.tools.avr-gcc.path}\bin\avr-g++" -c -g -Os -w -std=gnu++11 -fpermissive -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -flto -w -x c++ -E -CC -mmcu=atmega2560 -DF_CPU=16000000L -DARDUINO=106011 -DARDUINO_AVR_MEGA2560 -DARDUINO_ARCH_AVR -I"D:\Program Files (x86)\Arduino\hardware\arduino\avr\cores\arduino" -I"D:\Program Files (x86)\Arduino\hardware\arduino\avr\variants\mega" 0\BatteryCharger.cpp" -o "nul"
The system cannot find the file specified
     Preprocess: "{runtime.tools.avr-gcc.path}\bin\avr-g++" -c -g -Os -w -std=gnu++11 -fpermissive -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -flto -w -x c++ -E -CC -mmcu=atmega2560 -DF_CPU=16000000L -DARDUINO=106011 -DARDUINO_AVR_MEGA2560 -DARDUINO_ARCH_AVR -I"D:\Program Files (x86)\Arduino\hardware\arduino\avr\cores\arduino" -I"D:\Program Files (x86)\Arduino\hardware\arduino\avr\variants\mega" 0\BatteryCharger.cpp" -o "nul"
   Object reference not set to an instance of an object

Right before the update there were no compiler errors.
The folders all seem correct and contain the files.
I also notice that ""vMicro->Compiler->Deep Search Includes" if OFF and I'm not able to switch it on.

Any thoughts?

Sorry, forgot to mention that, but I did rescanning (menu vMicro -> Board pulldown -> Find or install a board--> Rescan) several times after searching the forum. The output screen shows "Toolchain reload complete".
(I read the message "PLEASE NOTE: Upgrading Arduino IDE to 1.6.11 can cause compile errors. In that case open the "Visual Micro Explorer > Board Manager" then click the Rescan button twice. After that there should be no problems. Please report to the forum if you encounter other issues. Version 1609.4.3 + of Visual Micro is required for Arduino 1.6.11+")

The solution only has 1 project: The solution Explorer says: "Solution BatteryCharger (1 project)". 

First I updated vMicro to the latest version.
In the release notes I saw a reference to some issues with the latest Arduino IDE that were fixed in this release.
I was on Arduino IDE V1.6.9 and then updated to V1.6.11, which is the version I'm having installed now.

Then started VisStudio and then the mentioned error occurred.

And yes, I tried "Build -> Clean Solution" a few times and then selecting "Build -> Rebuild Solution". Same error.

Would something drastic like uninstall Arduino, uninstall VisStud and then reinstalling everything do the trick?

I'm so sorry. You're helping me out so well and now I failed to ZIP the arduino15-folder for you.
(I was to eager in following your steps, so didn't read ahead...)
Even tried to use some recover-software but that only gave corrupted files... 

But you DID give the correct solution: The error message is gone.
Thanks for your quick support.