I have previously checked the PDFs - at random now I've gone to one and checked: Properties/security and found that
Full Control, Modify, Read & Execute, Read, Write are all ticked.
Is that sufficient?
But, I think that we have established that PDFs protected or unprotected cannot have the same annotation as an epub.
See this:
https://www.youtube.com/watch?v=A7SQepOdim8
So...thanks for the help to everyone, but it's an issue for Kobo to sort out.