I have tried to do the same but with .avi as choice. Video was in copy mode, audio was in aac mode without additional configurations and filters. I got file of duration that is twice shorter than original and audio was not in sync.sound but no image. The file was twice shorter than original.
I tried again to do the same with mp4 as my choice. Video was in copy mode and audio was in aac mode without additional configurations and filters. I g
Note: During opening of mkv I was asked to rebuild frame which I confirmed as yes. IN both cases I used the same .mkv file as source.
Thanks,
veki