I found a program called “HD Video Converter Factory Pro” that let me convert an MKV file to MP4 while preserving the different audio tracks. I tested it on my computer and I was able to change the audio tracks. Though I wasn’t able to do this on the Blu-Ray player via USB.
So looks like I’d need to find a way to convert it to a Blu-Ray format where it would function like a Blu-Ray disc and let you select different audio tracks.