Know you asked this question a long time ago and hope you found an answer. I'm having issues too. It appears that the bookmarks you make for a preview file are fixed to that file and it's location when you create the bookmark. If you move the file, the bookmarks remain but are not active. Look at the file trail and it will tell you where your doc was when preview created the bookmark. If you return the file to that location, to that folder (in my case I actually recreated the file trail and the old folder)...your bookmarks reappear.