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FFMPEG atempo fails due to padding


I have ripped a TV show from 2 sources (one pal and the other is NTSC). I would like to merge them into a single mkv file. The problem is that the audio tracks are not the same duration. They have different length of padding at amthe end, so if I run the atempo filter, there is a sync issue.

How could I fix this issue? (I would prefer a batch solution)

Thank you for your answers

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