I believe this is not the best tool to do the conversion from the command-line, it is not designed to be used this way.
This tool depends on zenity(which shows the graphical part) and processes files one-by-one, this is an excerpt from the README file provided by the tool
to use it as a plain bash script, provided you have access to an x session and have zenity installed, simply type: path/to/audio-convert path/to/filename... and specify as many filenames as you want. they will be processed one by one, just as it happens when you select multiple files on nautilus or rox.
I would suggest that you use the tools used by the script you mentioned, which is faac for AAC encoding, but you will have to decode FLAC files first, using flac.
For details about calling faac and flac from the terminal, you can look up online documentation, you will find many examples as they are commonly used, and you can also check the functions aac_encode() and flac_decode() in the script audio-convert:
flac_decode ()
{
temp_file=`echo "$1" | sed 's/\.\w*$/'.wav'/'`
flac -d "$1" -o "$temp_file" 2>&1 | awk -vRS='\r' -F':' '!/done/{gsub(/ /,"");gsub(/% complete/,"");if(NR>1)print $2; fflush();}' | zenity --progress --title="$title" --text="$2 $1" --auto-close
}
and
aac_encode ()
{
if [ $fields -eq 0 ] || [ $pass_metatags -eq 0 ]
then
aac_parse_fields
faac -w "${aac_fields[@]}" -q $quality -o "$3" "$2" 2>&1 | awk -vRS='\r' '(NR>1){gsub(/%/," ");print $3; fflush();}' | zenity --progress --title="$title" --text="$conversion $1" --auto-close
else
faac -q $quality -o "$3" "$2" 2>&1 | awk -vRS='\r' '(NR>1){gsub(/%/," ");print $3; fflush();}' | zenity --progress --title="$title" --text="$conversion $1" --auto-close
fi
}
but keep in mind you can't use them as is from audio-convert because they depend on other variables defined in the file.