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So lets say I have an MKV, and it has and audio track with a -21ms delay. If I import the audio from that MKV into Audacity, will it take the delay into account and chop off the first 21ms automatically? Also is there a way to check if any delays are set in an MKV?
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An MKV container can't apply a negative delay. It's likely that the program you're using for muxing is actually trimming 21ms from the start of the audio track. So if you demux and import into Audacity it will already be missing the 21ms.
MediaInfo can show when a positive delay is being applied by the container but it can't show when a file has been trimmed by applying a negative 'delay'.