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But I never need to mess with audio, so how would I just go about setting it to mux without re-encode?
becouse right now I use mkvmergeGUI to mux ac3 after meGUI completes the video job.
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Go to the tools menu - muxer - mkv muxer. This is your access ot the mkv muxer. And the next time you're encoding, make use of the autoencoding mode.. then when you're in the window where you define the name of your final file, you can check a checkbox at the bottom.. then when you press queue, the muxer window comes up again, with certain things already filled in.. then you can select your AC3 file.. that way it will only be muxed.