Last night I reset my device as well as deleted the media.xml from the Sony. (and rebooted my computer.)
Edbro is right, it isn't the Calibre dbase that is the problem. For some reason, Calibre stops reading the Sony dbase file. Today, after some sleep and caffeine, this finally sank in.
The metadata changes are in the Calibre files--which are all ok. (I did do a copy of all the folders over to my external HD last night, just in case.)
I think I've fixed it. I shut down Calibre. Used Explorer to delete all the file folders under database>media>books, and also media.xml. Unplugged the Sony from my computer, reset it and turned back on. Then connected it back up, turned on Calibre and it seems to be working fine now. I now have to move the books back over from the Library to the reader, but at least all the metadata changes I've made via Calibre are still there.