Transcode Apple ProRes

I am working through the tutorial at https://msdn.microsoft.com/en-us/library/windows/desktop/ff819476(v=vs.85).aspx because I need to write a program to transcode Apple ProRes files to H.264. The program does not work. Can anyone advise me how to do this? The program works on an already transcoded file, but not the original ProRes files. This is what ffmpeg has to say about the format:

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'Pan 1-15_05_15R_14_2.mov':
  Metadata:
    major_brand     : qt
    minor_version   : 537199360
    compatible_brands: qt
    creation_time   : 2015-05-15 17:51:39
  Duration: 00:01:34.43, start: 0.000000, bitrate: 140392 kb/s
    Stream #0:0(eng): Audio: pcm_s24le (in24 / 0x34326E69), 48000 Hz, 1 channels, s32 (24 bit), 1152 kb/s (default)
    Metadata:
      creation_time   : 2015-05-15 17:51:39
      handler_name    : Linux Alias Data Handler
    Stream #0:1(eng): Audio: pcm_s24le (in24 / 0x34326E69), 48000 Hz, 1 channels, s32 (24 bit), 1152 kb/s (default)
    Metadata:
      creation_time   : 2015-05-15 17:51:39
      handler_name    : Linux Alias Data Handler
    Stream #0:2(eng): Video: prores (apcn / 0x6E637061), yuv422p10le, 1920x1080, 138086 kb/s, 29.97 fps, 29.97 tbr, 2997 tbn, 2997 tbc (default)
    Metadata:
      creation_time   : 2015-05-15 17:51:39
      handler_name    : Linux Alias Data Handler
      encoder         : Apple ProRes 422
      timecode        : 17:51:39:00
    Stream #0:3(eng): Data: none (tmcd / 0x64636D74)
    Metadata:
      rotate          : 0
      creation_time   : 2015-05-15 17:51:39
      handler_name    : Libquicktime Time Code Media Handler
      reel_name       : 001
      timecode        : 17:51:39:00
Unsupported codec with id 0 for input stream 3

Thanks.