I can confirm after installation of the KB2921525 (replace compiler) , I also got the error
fatal error LNK1262: link failed due to mismatched versions of 'C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\ce\bin\x86_arm\c2.dll' and LINK.EXE
I tried to fix the error by installing the KB3029264 (replace compiler, linker and assembler), only to end up with a different error:
fatal error C1047: The object or library file '..\..\libs\lib\Toradex_CE600 (ARMv4I)Release\\SysInfoLib.lib' was created with an older compiler than other objects; rebuild old objects and libraries
The optimization we activated for the V2.1 release is incompatible with different compiler/linker versions. We will soon release a new version of the Libraries (V2.2) with that optimization disabled. The library will then behave again like in Release V2.0 and older.
So far, as a workaround, you either need to use the debug version of the libraries, or uninstall the KB2921525.
If for any reason the uninstall fails, the original compiler/linker are stored in a backup folder
C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\ce\bin\x86_arm\KB2921525_BACKUP\