Yes, it's kind of tough, you'll lose everything when you upload a fid tree generated with mp3tofid. On the other hand, if you don't like the result; you can continue with emplode or jemplode without losing everything again. If you then go back to mp3tofid again, you'll lose whatever you changed with (j)emplode.
If you just want to try mp3tofid without losing your data, and you have enough diskspace, you can rename you current fidtree and database files to something the player will ignore. Make sure you don't lose this backup tree when you start rsyncing. Use --dry-run before you --delete.
Pim