I have Matroska file with some subtitles already built in. How can I add another subtitles, with proper language setting and encoding?

Tried:

mkvmerge -o output.mkv -S source.mkv new-subtitles.srt

but it looks like it removed all other subtitles. What am I doing wrong?

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That is because you specified the -S parameter when pointing to the source file. -S removes all subtitle tracks from input. What you want is actually this

mkvmerge -o myouput.mkv myinput.mkv --language "0:ger" --track-name "0:mytrackname" -s 0 -D -A mynewsubtitles.srt

This will append mynewsubtitles as the last track with that trackname and language. Also in current versions of mkvmerge the default language is english. So you do not need to set --language if that is the case.

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