FFMPEG and a simple bash script will get the job done. FFMPEG is the same set of libraries that are included with products like Handbrake.
The basic syntax is very simple:
ffmpeg -i inputfile outputfile
If you wanted to convert a FLAC to MP4, you would simply enter
ffmpeg -i inputfile.FLAC to outputfile.MP4
To convert a number of files a simple bash script like the one below will convert
for file in /foo/bar/*.mp3
do
fullfilename=$(basename "${file}")
filename="${fullfilename%.*}"
ffmpeg -i "$file" "/foo/bar/converted/$filename.mp4"
done
This basic script parses through a directory, takes the original filename, then removes the extension so a new extension can be added during output.