I have 2 files I would like to merge:
1) MKV file, 23.976fps, 2h04 length
and one audio file extracted from an AVI using VLC
2) MP3 file from AVI 20fps, 1h59 length
The audio track is from the same movie but a different language. I could use MKVToolnix I guess but how can I sync the audio file to the new framerate/time length?
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Drop both into mkvtoolnix gui and deactive the unneeded tracks. Then select the video track and change fps to 25(*). Mux and see if it is sync. If it is not sync, try to find the delay and use that on the audio track. If you cannot get it right using the above methods the cuts might be different (like cinema versus director's cut) and it will become much more difficult.
((*) changing video fps is easier than changing audio fps. for audio fps change a re-encoding might be necessary for a clean result.)