Marking up and keeping PDF markups permanent has always been a difficult process. PDFs are designed to be made as originals and then remain. This is why PDFs have all of the signature features, etc. which you can make to sign documents and call it secure from that point. (I meant the actual security signatures, not the stamps). There are even stories where the CIA and NSA have made redactions and then people would print them, and the words were still there. Not good.
Here is one way, although it is an extra step. And, you can't do it with sticky notes. They are just what they say: sticky. And, they can be unstuck.
But, if you use the red outliners or typewriter to mark things up or the highlighters and underliners and THEN print that document to PDF, the changes are there forever. They are now part of the document.
