Matroska audio (.mka) files are often used to store movie audio tracks outside of more usual Matroska container, typically to store alternative language localization to a movie and so on.
In case you want to transform these tracks to FLAC format, i.e. perform mka to flac conversion, you will have to use to Freemake Audio Converter or similar program. Just keep in mind that the resulting quality won't improve, as the audio track within .mka file was probably compressed already with a lossy method.Open MKA file Open FLAC file
A popular free audio converter
A multimedia converting tool for Windows