ac3 to aac lib_fdk

# assuming you have the source as a mkv and the audio is the second track
mkvextract tracks souce.mkv  1:souce.ac3
ffmpeg -i source.ac3 -c:a libfdk_aac -vbr 3 -ac 6 source.aac

# and that you're adding it into an existing encode (because you forgot to say no-audio)
mkvmerge -o source.mkv --language 0:eng --track-name 0:English source.aac
mkvmerge -o --audio-tracks 2 

mv movie.mkv