@jws Another case of Sierra's PDF bug: Every 2 months I submit an annotated crossword puzzle for publication in the Mac User Group's monthly magazine. The last two issues, December & March (no January edition) have had the annotation layer stripped out in the process of emailing it to the editor.
So in future I'm going the export the annotated PDF as another PDF (this flattens the annotations layer & fixes it to the rest of the image) and send the editor both a zipped file & a Droplr link of the same. http://d.pr/f/6tLC