I have a laptop with the Sony eLibrary on it.
I think it is like you said.."..the software just build a database pointing to the original location.."
The files on my laptop are located in My Documents / My Digital Editions / eBook Library
The ebook files are shown like this ..... cbuscehch000070g
I am not sure what happens if you rename the file (in this location) to the title of the book.
I hope this helps.