Ok, I know you can use AVIdemux, but when I try it, the audio is out of sync. Is there a program that edits an MKV file as well as all the tracks including subtitles?
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Anime on Laserdisc is teh awesome
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Not really, because MKV is not built for editing, and no serious editing tool will work with it. Try a couple of different version of AVI Demux and see if one works better than the others. Otherwise look at converting the mkv to something like m2ts (should be do-able without re-encoding) and see if you can work with that format instead. Of course the next issue you will face is that very few editors will work with H264 without re-encoding it.
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I use Virtualdub. There are two options. You will need the MKV plugin from fcchandler, aac plugin from fcchandler, x264vfw and MKVtoolnix (mkvmerge).
Option one: Make your cuts > choose Video > Compression > x264vfw > Smart Render > Audio > Direct Stream Copy > Save Avi > open AVI with MKVmerge and mux to MKV.
Option two: Open mkv in Virtualdub > move to first cut and note time (example: 0:00:13.019), move to last cut and note time (example:0:51:55.546). Open mkv in MKVmerge and choose Global > click Enable splitting > tick After time codes > enter 00:00:13.019,00:51:55.546 > under maximum number of files enter 3 > click Start muxing. Three files will be created. The intro, the movie and the credits.
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