I am using ubuntu 16.04's default pdf viewer (evince) to annotate pdf files. I have saved a copy of the PDF but unfortunately none of my annotations appear in the new copy. I still have the annotated file open but am scared of closing it for fear of loosing my annotations. Is there some other way I can save with annotations? is there some location where the annotations files get stored temporarily?
I had the same problem and unfortunately could not solve it, but instead lost all my annotations. The reason for this was, however, that I directly opened the pdf file from Thunderbird Mail Client, where it was attached to an EMail. Saving copies only saved the original pdf without any annotations.
After saving the attached pdf first and then opening it via file manager, I was able to save copies with their annotations.