If you add annotations to a PDF, sync, and then don't see your annotations anymore, please check your PDF is not protected.

You can open it on your desktop using Adobe reader or Preview, and try to add annotations.

If you see you need to duplicate the PDF document to save annotations, it means it is protected and won't work with PaperShip annotations.

In this case, please upload an unprotected version of this PDF in your library to be able to add annotations.