Convert MKA to FLAC

You can absolutely convert Matroska Audio Files directly to Free Lossless Audio Codec Files (.mka to .flac conversion), since both files types are well supported

Use tools, such as Nero Recode or Helium Music Manager, which allow users to easily import MKA audio and export it in FLAC.

Just keep in mind that the resulting quality will not improve, as your MKA file has probably been already compressed with a lossy method.