Thanks for your reply! This is what I found out:
Where are my ebook files located?
The Sony Library doesn’t move files "into" the Library, the Library just maintains a pointer to the actual file on your hard drive or other media.
If you downloaded them using ADE, the folder is <your username>/documents/My Digital Editions
If you downloaded them using the sony software, the folder is <your username>/documents/My Books/Reader Library
This is an xml file that stores any annotations.