[Zubersoft]

You can embed them in the underlying PDF if you want those changes to be shared by every song that uses that PDF. You will lose access to some features with embedded annotations (and you have to enable the option to allow editing of embedded PDF annotations if you need to edit them), but if you don't really need to edit those annotations after the fact, then this won't be an issue. Perhaps in the future I'll support a way to link annotations between songs using the same PDF, or at the very least, a way to copy annotations from one song to another, so that embedding isn't necessary.

Mike