If using "Open file" from ReadCube Papers to read and add annotation a paper in Preview (Mac) (the location of that paper is in ~/Documents/Papers Library), hit save, and then close Preview, the change won't be reflected in ReadCube Papers, instead, it will try to recover the file to an earlier version, which led to the lost of all the annotation made by Preview. Please fixed that since not everyone like the internal PDF reader, and there do exist people have there preference over PDF readers.
Very strongly agree.
What I'm currently having to do is to download the PDF to outside of the Library (to get any annotations made on the web), edit the PDF locally (in Preview or Highlights), attach it to the reference, make it the primary attachment, and then finally delete the old attachment.
I think Papers is storing the annotations outside of the PDF so that it has a clean copy in case it needs one perhaps. There has to be a way to allow it to do that and still do end-to-end synchronisation of annotations.