[Alan Evans]

You do have the right idea - swapping the new file in is the best approach (Long press song->Swap File).  If you want to experiment with this, you can copy the song first, and then swap the file in the copy to make sure it works the way you want.  Are you encountering errors while trying to do this?

If I am doing it correctly, the (new) song that I'm swapping the old one with is not showing the annotations. Perhaps the order I'm doing things is not correct.