Certainly the proof of the pudding is in the eating.

Simple MP3 to FLAC isnt going to do anything other make a larger file of the same quality.

There are however ways of cleaning up audio files of any format. I use Logic Pro to record but it is also excellent at making background hiss go away, clicks and pops disappear and if I wish, enhancing.

Ok, it may introduce a blend that wasnt on the original, but if your ears cant tell, then great.

After all, every single recording ever has buggered about with the integrity of the musician in the studio's acoustic sound to begin with.