Get what track we need to modify

mkvinfo <filename>

The first track is usually video, so focus on the next tracks that have a type of audio

| + Track
|  + Track number: 2 (track ID for mkvmerge & mkvextract: 1)
|  + Track UID: 1764244740875200000
|  + Track type: audio
|  + Language: ger
|  + Codec ID: A_AAC
|  + Codec's private data: size 2
|  + Default duration: 00:00:00.021333333 (46.875 frames/fields per second for a video track)
|  + Language (IETF BCP 47): de
|  + Audio track
|   + Sampling frequency: 48000
|   + Channels: 2
| + Track
|  + Track number: 3 (track ID for mkvmerge & mkvextract: 2)
|  + Track UID: 8879447932733370000
|  + Track type: audio
|  + "Default track" flag: 0
|  + Codec ID: A_EAC3
|  + Default duration: 00:00:00.032000000 (31.250 frames/fields per second for a video track)
|  + Language (IETF BCP 47): en
|  + Audio track
|   + Sampling frequency: 48000
|   + Channels: 6

Now we can set the default track (Which some software doesn't seem to respect)

mkvpropedit <filename> --edit track:3  --set flag-default=1 --edit track:2 --set flag-default=0

Then I flip the track numbers so that the software previously mentioned will just play what I want

mkvpropedit <filename> --edit track:3  --set track-number=2 --edit track:2 --set track-number=3