appear in the XML file with an "'" instead of the apostrophe in the filename. These were not recognised by Bookends.
Search/replace through the XML file replacing all "'" with a single apostrophe seems to have solved the problem, and now bookends attaches the right PDF. Replacing it with "'" also did the job.
I think this is actually a bug in Papers, as I think this is what you would use if the filename actually contained "'" in it, which very few do...
In any case, it would be better if this happened on its own if you'd like lots of people to do his transision
