Most likely you can do this with ffmpeg but you'll need to understand the command line.
It could be as simple as:
ffmpeg -i INPUT.mka OUTPUT.flac
Video: JVC RS4500 135" screen in pure black room no light, htpc nvidia 1080ti.
Audio: Anthem mrx720 running 7.1.4, McIntosh MC-303, MC-152, B&W 802d3 LR, B&W HTM1D3 center, B&W 805d3 surround, B&W 702S2 rear, B&W 706s2 x 4 shelf mounted for atmos, 2 sub arrays both infinite baffle: 4x15 fi audio running on behringer ep4000 + 4x12 fi audio running on 2nd ep4000.