Thank you for explaining.
I encode the FLAC files to AAC in the end. It would probably be more efficient to just extract the tracks with eac3to and then downmix and encode them directly with the audio encoder in MeGui, but back when HD-DVDs and BDs started coming out eac3to was the only tool I had that could decode some of the tracks and also could do the processing I needed. That's how I ended up with that workflow.
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