I've had this problem all day. Doing lots of annotation in a pdf file, almost 50 pages, using the EN annotating tool. Saving and exiting works for a bit, but then it seems to lose the file. I can see the note in the note List but the note itself appears completely empty. I have tried using Note history and restoring different versions, and starting from scratch with new files, the same thing happens. When I delete the notes and view in Trash I can see - in the left hand Note List - a tiny thumbnail of the pdfs (and I can spot annotations in it) but again the right hand note itself appears empty.
Just upgraded precisely in order to annotate PDFs, to be more productive ...erk ?
Any help greatly appreciated