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I would recommend using a GUI for this instead. The issue with using the CLI is that mkvmerge works mainly with track ids, and I'm assuming not every single one of your MKVs are identically mapped, so accounting for all the variables just becomes too much work. Check out MKV Muxing Batch: https://github.com/yaser01/mkv-muxing-batch-gui
jmkvpropedit is a lovely tool that i've been using for years to do this.
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