The resulting command looked good at first sight, something like „mkvmerge -o output.mkv first.mkv —-no—video -s 1 -a 2 -a 3 -a 4“. The problem here is that there can only be one -a flag, so it should have been „-a 2,3,4“ instead. But mkvmerge didn’t really care and just discarded every -a flag except the last one. So I ended up with only one of the audio tracks copied over. I only noticed when I actually checked the resulting file that it had less audio tracks than it was supposed to.

This would not have happened to a human after studying the man page - the documentation is very clear about the -a flag and I have no idea what led ChatGPT to come to the conclusion it did.