WOW64 のファイル システム リダイレクタを制御するクラス ref: http://qiita.com/hirocueki/items/54e35f9aa1c7137b53cf

file0.cpp

class Wow64FsRedirectionService
{

    typedef BOOL ( WINAPI *fpWow64DisableWow64FsRedirection )( LPVOID* );
    typedef BOOL ( WINAPI *fpWow64RevertWow64FsRedirection )( LPVOID );

public:
    Wow64FsRedirectionService()
        : m_lpOldVar( nullptr )
        , m_fpWow64DisableWow64FsRedirection(nullptr)
        , m_fpWow64RevertWow64FsRedirection(nullptr)
    {
        m_hModule = ::LoadLibrary( _T( "Kernel32.dll" ) );
        if( m_hModule )
        {
            m_fpWow64DisableWow64FsRedirection  = (fpWow64DisableWow64FsRedirection)::GetProcAddress( m_hModule, "Wow64DisableWow64FsRedirection" );
            m_fpWow64RevertWow64FsRedirection   = (fpWow64RevertWow64FsRedirection)::GetProcAddress( m_hModule, "Wow64RevertWow64FsRedirection" );
        }
    }
    ~Wow64FsRedirectionService()
    {
        if ( m_hModule ) {
            // m_lpOldVar がnullptrではないとき => Wow64RevertWow64FsRedirection（リダイレクト有効化）が呼ばれていないので、もどしておく
            RevertRedirection();

            ::FreeLibrary(m_hModule);
            m_hModule = nullptr;
        }
    }

    void DisableRedirection() {
        if (m_fpWow64DisableWow64FsRedirection )
            m_fpWow64DisableWow64FsRedirection( &m_lpOldVar );
    }
    void RevertRedirection() {
        if (m_lpOldVar && m_fpWow64RevertWow64FsRedirection ) {
            m_fpWow64RevertWow64FsRedirection( m_lpOldVar );
            m_lpOldVar = nullptr;
        }
    }

private:
    LPVOID m_lpOldVar;
    HINSTANCE m_hModule;

    fpWow64DisableWow64FsRedirection m_fpWow64DisableWow64FsRedirection;
    fpWow64RevertWow64FsRedirection  m_fpWow64RevertWow64FsRedirection;
};

file1.cpp

void do()
{
  Wow64FsRedirectionService serv;
  serv.DisableRedirection();

  // リダイレクトされてしまうファイルパスへのアクセスはここに。

  serv.RevertRedirection();
}

file2.cpp

#include <functional>
class Wow64FsRedirectionService
{
    typedef std::function<void()> DisableScopeFunction;

    typedef BOOL ( WINAPI *fpWow64DisableWow64FsRedirection )( LPVOID* );
    typedef BOOL ( WINAPI *fpWow64RevertWow64FsRedirection )( LPVOID );

public:
    Wow64FsRedirectionService()
        : m_lpOldVar( nullptr )
        , m_fpWow64DisableWow64FsRedirection(nullptr)
        , m_fpWow64RevertWow64FsRedirection(nullptr)
    {
        m_hModule = ::LoadLibrary( _T( "Kernel32.dll" ) );
        if( m_hModule )
        {
            m_fpWow64DisableWow64FsRedirection  = (fpWow64DisableWow64FsRedirection)::GetProcAddress( m_hModule, "Wow64DisableWow64FsRedirection" );
            m_fpWow64RevertWow64FsRedirection   = (fpWow64RevertWow64FsRedirection)::GetProcAddress( m_hModule, "Wow64RevertWow64FsRedirection" );
        }
    }
    ~Wow64FsRedirectionService()
    {
        if ( m_hModule ) {
            ::FreeLibrary(m_hModule);
            m_hModule = nullptr;
        }
    }

    void UsingDisable(DisableScopeFunction dosomething) {

        if( DisableRedirection() )
        {
            dosomething();
            RevertRedirection();
        }
    }
private:
    bool DisableRedirection() {
        if ( !m_fpWow64DisableWow64FsRedirection )
            return false;

        return TRUE == m_fpWow64DisableWow64FsRedirection( &m_lpOldVar );
    }
    bool RevertRedirection() {
        if (!m_lpOldVar || !m_fpWow64RevertWow64FsRedirection ) 
            return false;

        const BOOL result = m_fpWow64RevertWow64FsRedirection( m_lpOldVar );
        m_lpOldVar = nullptr;
        return TRUE == result;
    }

private:
    LPVOID m_lpOldVar;
    HINSTANCE m_hModule;

    fpWow64DisableWow64FsRedirection m_fpWow64DisableWow64FsRedirection;
    fpWow64RevertWow64FsRedirection  m_fpWow64RevertWow64FsRedirection;
};

file3.cpp

Wow64FsRedirectionService FsRedirecta;
FsRedirecta.UsingDisable( [](){
  // リダイレクトされてしまうファイルパスへのアクセスはここに。
});