Maybe this is too late, but can the MKV file be made into an MP4 file?
I'm not all that familiar with Mac OS, but I'm assuming anything running on a Mac would be able to handle an MP4 file. You mentioned Avidemux, try using it to copy the audio and video streams into an MP4 container.
It may not work, MP4 cannot handle all the formats MKV can (and I think there are a couple that MP4 handles that MKV can't). You may lose any extra audio or subtitles that exist in the MKV file, because Avidemux seems to only handle a maximum of two audio streams

. In Windows, I like using Yamb.
Can you get FFmpeg on a Mac? It may need a command line, but it always seems to work for me.