Get file audio stream numbers

ffmpeg -i in.mp4

Stream #0:0: Video: ...
Stream #0:1: Audio: ...
Stream #0:2: Audio: ...

Then choose which ones you want with map:
ffmpeg -i in.mp4 -map 0:0 -map 0:2 -vcodec copy -acodec copy out.mp4

To synchronize video with audio:
Convert with Wondershare Uniconverter