LabVIEW can read and write binary files. This means there is no reason it cannot edit the MP3 files directly. The problem is that you will need to find the file format of MP3s on the web, so that you will know what data to expect, where it is, and how to change it. This is a non trivial task but great documentation would make the job much easier.
For your information, I looked on NI's site and did not find an existing program.