Download a program from here. install it. use MAM( Media asset management) for this purpose. There is a batch transcode program for it. But it will transcode full video, not part as desired by you.
http://casparcg.com/forum/viewtopic.php?f=5&t=783#p4193

I finally got it working by following ffmbc by following command. Thanks to baptiste.coudurier ffmbc-0.7.4-x64.exe -i inputhdfile -threads 4 -tff -target xdcamhd422 -f mxf -an output.mxf -acodec pcm_s24le -ar 48000 -newaudio -acodec pcm_s24le -ar 48000 -newaudio -map_audio_channel 0:1:0:0:1:0 -map_a...

I am able to achieve (with above command) every property of xdcam hd422 50i with ffmpeg except
Format settings, Matrix Custom
My file shows
Format settings, Matrix Default

Is there a solution to it?