I was annotating a .pdf and all was working just fine.. but when I did create a new (extra) page "New Page at the end" the .pdf disappeared. I only realized that all .pdf disappeared when I changed the page style to plain.
So, there are 2 possibilities for the behavior:
1. New page at the end when annotating a PDF
2. Change page style (after a new page at the end when annotating a PDF)
The attachment shows there are no more charts behind my annotations.