I'm not reverting the change. The specifications state explicitely that in case of an absent element its default value must be used instead. I'm not breaking compliance, I'm forcing others to fix their bugs.
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For example, have the video stream and audio stream, and 2 versions of the subtitles, "eng" and "rus", I point "rus" subtitles to be - default.
Then after muxing and adding to Mkvmegre GUI displays all streams in default track flag - no.
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That's indeed a bug in mkvmerge's handling of the files. I'll fix it.