To encode from FLAC to AAC, you have the choice to use:

• QAAC (by using Wine and following this tutorial for example)
• following this tutorial for fdkaac
• use another AAC encoder
  • but according to some people apple (QAAC) ≒ fdk-aac ＞ nero ≒ ffmpeg

It’s easy:

Extract the FLAC tracks from your videos

You need to have installed mkvmerge and mkvextract (for me, it’s included in mkvtoolnix-cli package).

$ mkvmerge -i 'Your_Video.mkv' 
File 'Your_Video.mkv': container: Matroska
Track ID 0: video (MPEG-4p10/AVC/H.264)
Track ID 1: audio (FLAC)
Track ID 2: subtitles (SubStationAlpha)
Attachment ID 1: type 'application/x-truetype-font', size 4288364 bytes, file name 'KozGoPro-Bold.ttf'
Chapters: 5 entries

So here we need to extract the track number 1 (audio FLAC):

$ mkvextract tracks "Your_Video.mkv" 1:You_Video_audio.flac

Then encode it!

You need to have installed ffmpeg and fdkaac packages

$ ffmpeg -i "You_Video_audio.flac" -acodec pcm_s24le -vn -sn -f wav - | fdkaac --bitrate-mode 5 --ignorelength -o "You_Video_audio.m4a" -

I use the highest quality using the highest possible value for bitrate-mode (which is 5)

Done!