Hello,
Handbrake is not working with the latest release of ffmpeg. This is a known issue and a fix is already in the upstream code for handbrake 1.3.0. Without this fix handbrake loses the audio track while encoding. The github issue can be fund here: <https://github.com/HandBrake/HandBrake/issues/2124> and the commit fixing it here: <https://github.com/HandBrake/HandBrake/pull/2126> I hope you're able to inclue this as a patch in the downstream handbrake package.

Cheers,
Jannik

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