I have been using adobe acrobat do to notes/highlights before and when I have opened the document in e.g. Preview, I could see the highlights and notes I have added. It is not the case with Skim, is there any way to actually incorporate the changes into the pdf?
see faq
work-around here: https://apple.stackexchange.com/questions/79429/make-skim-save-pdfs-with-embedded-notes-by-default