Audacity uses FFMPEG to work with flac files, since it’s only going to convert them might as well go directly with FFMPEG

Or use Shutter Encoder, it’s basically FFMPEG with a GUI (altough with 1.7.3 I’ve run into problems with some codecs, use 1.7.2)

But for this it might be easier to just script it than drag and drop every file, depends on OP