I was able to find what I was looking for, here is how I did it.
To convert the audio part of the mkv file I used - Pazera Free Audio Extractor - You could also use TFM Audio Tool
After you have converted the audio file you can recombine the audio file and video file with MKVToolNix - be sure to deselect the audio track that is already in the mkv file, or set the new audio track to default, before muxing it all together.