When the user saves a pdf with annotations (he just made) he may think the annotations are saved within the document. I'd say that a dialog should ask the user if he really want to save a identical copy of the pdf or wheter he wants to export the annotations in a .okular file. Don't say that he need to read the documentation, because this behaviour is really confusing even to an expert user.
Isn't this a duplicate of Bug 268575? https://bugs.kde.org/show_bug.cgi?id=268575
Yes I think those can be merged. I hope this is fixed soon because the UX is horrible. *** This bug has been marked as a duplicate of bug 268575 ***