Visual Studio 2013 deletes header files (and more?) of libraries.

Sorry if my question is not directly about windows programming, but more about VS2013, but I guess a lot of you may be working with it, since it's windows only (I think) so I'm just going to try asking it here :)

Just compiled the google protocol buffer files using the provided *.sln file, decided to run the "Clean Solution" command because I got some errors and wanted to start over after fixing them.
Everything worked fine, got my *.lib files, got back to my main project and.... got a lot of errors for missing *.h and *.hpp files.
So I check the folders and it turns out all the header files of boost and Box2D are GONE! What???
How can this happen? I ran an antivirus check, didn't find anything. If it was a virus why would it only target and delete header files and random folders inside boost and Box2D (but not the *.lib files)? Everything else is normal.
I definitely didn't delete anything manually, so i suspect VS2013 must have deleted them all. Why does this happen?
Did "Clean Solution" do this? But why? It didn't even have any references to my boost and box2d header files in the google protoc project file.
Luckily windows was able to restore the folders to their previous versions where everything was still fine... I don't even know if anything else got deleted, but doesn't seem like it. I would still really like to know how this happened so I can avoid it in the future. Any ideas?
All that I did was add the /FS compiler option (Forces writes to the program database (PDB) file to be serialized through MSPDBSRV.EXE.) and "Clean Solution".
Could it be that Visual Studio has nothing to do with this? But then I dont have any clue what else could be the cause.
My *.h and *.lib files are located in C:\boost and C:\Box2D etc.
Loaded the solution file at
C:\Users\****\Desktop\protobuf-2.6.0\protobuf-2.6.0\vsprojects
Output was set to:
C:\Users\****\Desktop\protobuf-2.6.0\protobuf-2.6.0\vsprojects\Debug
and
C:\Users\****\Desktop\protobuf-2.6.0\protobuf-2.6.0\vsprojects\Release

Edit:
Ok I guess it's not Visual Studios fault...
More files are missing, the culprit seems to be tests.exe provided by google protobuffers. At least according to the Comodo Defense+ Logs.
For whatever reason it didn't just test if the compilation of protobuffers was successful but also went full berserk and deleted COMPLETELY random files on my computer.
Thanks google!
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