mkvextract tracks /path/to/matroska.file.mkv 2:/tmp/dts.file.dts
dcadec -o wavall /tmp/dts.file.dts | aften - /tmp/ac3.file.ac3
mkvmerge -o /tmp/matroska.file.mkv /path/to/matroska.file.mkv /tmp/ac3.file.ac3
Another way is to use this to extract and remerge the stream automatically.
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