Depending on what is in the Matroska file, you may not need to decode it, just remux.
I assume the video, for example, is H264, so just do it. Below is an example of a pipeline for gst-launch for remapping a file with h264 and mp3.
gst-launch-0.10 -v filesrc location=$file \
! matroskademux name="demux" demux. ! h264parse ! queue \
! mp4mux name=mux ! filesink location=$file._out.mp4 demux. \
! mp3parse ! queue ! mux.`
You can also watch the Transcageddon transcoder (www.linuxrising.org), which should give you a wish.
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