This exporting highlight to Jarnal thing is an exciting possibility, I've downloaded the stuff and will try it soon. I was using Xournal but could switch to Jarnal if this works.
In the meanwhile, I'm wondering if I wanted to save my Sony PRS-600 highlights, if I could simply store its internal files and then load them back in when I want to view that pdf and its highlights at a later time. That is, I have a lot of pdf files, and don't want to keep them all inside the Reader. When I'm done reading and highlighting, can I just copy them to my hard drive, and later, copy them back to reader and view the highlights.
I'm going to try this manually, but maybe one of you guys has (or can create) a script where you point to the pdf folder or name within the sony reader, and it just extracts all the necessary files onto your hard drive from the reader.
Wouldn't that be useful to anyone? I've only created the most basic scripts but if nobody more knowledgeable than me is willing to help, I can have a shot at it, if there is demand for it.