mkvtoolnix is the best tool for this stuff. iirc ffmpeg has some limitations in this area
Okay, looks like you can do it in ffmpeg, but you have to map every audio stream individually in the command to rearrange them.
I believe you can remove (default) with -disposition:stream 0 so, if you have three subtitle tracks, all marked as default, and you want only second with that mark, you'd do something like this:
ffmpeg -i input.mkv -c copy -disposition:s:0 0 -disposition:s:2 0 output.mkv
And if you want to mark a stream as default, you do -disposition:stream default.
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