MKV file has 2 audio streams (#2 is FLAC). (I'm not sure what it means when 2 audio streams are listed.) Anyway, I cut MKV in avidemux and file seemed corrupt. #2 audio stream info stated "undef" and "128 kbps". I suppose audio was corrupt? (fyi: Original MKV file w/FLAC plays in VLC Player.)
In order to cut MKV w/FLAC in avidemux do I need to demux, cut audio separately, then remux (using mp3 or FLAC)?
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Try cutting/splitting with MKVMergeGUI. It has splitting options under the Global tab and it can append split sections if need be. It's not "editing" friendly as there's no preview so you ned to use a media player to find your split points. Whatever point you specify for splitting, it'll split on the following keyframe (which is normal). You can also delete the second audio stream if you don't want it.
Or Video To Video converter has a "commercial remover" under the Tools menu which provides a preview for splitting. The video still needs to be cut on keyframes if you don't want to re-encode, but it'll take care of that for you. Once you've finished editing, select okay and choose "direct stream copy" from the list of conversion presets, then Convert. You're not actually converting though, unless you tell it to.