What do you mean with "mark something"?

If you mean: what happens if I use mp3tofid/rsync, then upload someting with emplode, and then again with mp3tofid/rsync, then the answer is:

You lose all the changes you made with emplode.

But if you add your newly uploaded tune to your source tree on your host PC as well, it will be re-uploaded, but very likely with a different FID number. If you manage to rename your new tune on the player so it gets the same FID number as mp3tofid thinks it should have, then rsync will not have to re-upload the tune.

Needless to say, mp3tofid/rsync are best used exclusively in order to be of any use.

You can easily try mp3tofid "running dry". Nothing happens on your player until you use rsync to actually transfer the data. Add something to your source tree, or change some ID3 tags and see how mp3tofid notices.

Pim