You don't need to worry about the particular structure of the files if you break the files into fixed-size chunks (e.g. 512KB) and do the dedup based on the chu

You don't need to worry about the particular structure of the files if you break the files into fixed-size chunks (e.g. 512KB) and do the dedup based on the chunks. The difference in the metadata of MP3 will be just in the first chunk, and the rest will be exactly the same no matter how you change the ID3 data. This strategy works for many other types of media files, too.