I'm looking for a way to join two .MKV's without loosing the multiple audio and subtitle tracks held therein. From what I've done, re-encoding, even directly to another .MKV would wipe the extra data. Is my only option to extract them from the file and then add them back in after I encode? Or is that even possible? Thanks in advance.
		
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	Try Mkvmergegui. Use the append-button to add the second mkv. Click start muxing to make a new mkv. 
 
 I don't know how it handles the subtitles timing though...maybe you have to fix/join/resync them with something else.
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