You shouldn't use both the sony software and libprs500 to manage books on your reader.
The way libprs500 manages metadata on the device is by writing your custom metadata to a XML file on the reader which the reader uses to present the list of books. Unfortunately, if you reboot the device, remove the card, etc, this file is replaced by an automatically generated list of books that uses metadata from the files themselves, causing you to lose your changes. If you read only LRF format books, one possible solution is to first edit the metadata in the libprs500 library view, and then upload the books to the device. The newly uploaded books will have the metadata in both the book file and the XML file, so the metadata should persist.
NOTE; You should use a recent version of libprs500 for the above.