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Did you try ffmpeg? I've heard it doesn't have the best AAC/ALAC encoder but at least try it. Also if you need to batch convert all of your library you'll need to write some sort of a script to do that, because ffmpeg is a CLI program. You're using Linux so it wouldn't be a problem, I assume.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.