[Zubersoft]

This has come up in the past and it's something I want to address when I have time. I agree that it will be useful to be able to have a concept of private layers, or a way of indicating what layers should be synchronized (this assumes the same layer name is used across all scores though). As far as your question, users can turn off the visibility of specific layers, so you would either need to have users turn off the visibility of the layers they don't want, or you'd have to choose not to synchronize annotations at the moment.

Mike