Get the track information

mkvmerge -i /path/to/matroska.file.mkv

Sample output

Track ID 1: video (V_MPEG4/ISO/AVC)
Track ID 2: audio (A_DTS)

This means that the matroska.file.mkv contains two tracks, a video track with id 1 and a DTS track with id 2.

Extract the DTS track

2 is the DTS track ID from the given example.

mkvextract tracks /path/to/matroska.file.mkv 2:/tmp/dts.file.dts

Converting the DTS track to AC3

dcadec -o wavall /tmp/dts.file.dts | aften - /tmp/ac3.file.ac3

Remux the AC3 track into MKV

mkvmerge -o /tmp/matroska.file.mkv /path/to/matroska.file.mkv /tmp/ac3.file.ac3

Verify

mkvmerge -i /tmp/matroska.file.mkv

Sample output

Track ID 1: video (V_MPEG4/ISO/AVC)
Track ID 2: audio (A_DTS)
Track ID 3: audio (A_AC3)

Delete temporary files

rm /tmp/dts.file.dts
/tmp/ac3.file.ac3

Remove the DTS track

3 is the AC3 Track ID from the given example (see Verify)

mkvmerge -o /tmp/matroska.file.ac3.only.mkv -a 3 /tmp/matroska.file.mkv