title doesn't say why you need mp3, therefore I say you should use ogg vorbis. in which case you'd only have to specify the flac files and it would encode based on those.
for mp3 I can point you to BladeEnc
, which I've used in the past, but it's no longer developed and even the home page wants you to use ogg vorbis. if you don't REALLY need mp3 you might take this not so subtle hint. you might also have to extract the flacs to wav to work with the encoder, I wrote a script to do this, but it was for mp3 to vorbis, and would require some editing. tell me if you want it.