Convert FLAC to MKA

There are some audio editing programs and (online) converters that support both file formats, which means that converting Free Lossless Audio Codec Files directly to Matroska Audio Files (.flac to .mka conversion) is certainly possible.

It seems your best option is using Freemake Audio Converter or Freemake Video Converter, which should perfectly capable of converting FLAC audio files to MKA format.