Skip AAC but convert all other audio to AAC while remuxing MKV to mp4

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You will need to create a custom profile to do this. MCEBuddy can differentiate between AC3 and non AC3 input streams. See this topic for details:

Basically depending on whether you’re using Handbrake or FFMPEG you would need something like this, this keeps non AC-3 audio stream as is and converts AC3 audio into AAC

handbrake-audioac3=-E faac -R auto -B 384 -a 1,2,3,4,5
handbrake-audio=-E copy -a 1,2,3,4,5

AND/OR

ffmpeg-audio=-acodec copy -map 0:a
ffmpeg-audioac3=-acodec libfdk_aac -ab 384k -map 0:a