I figured out how to make it work.
What was happening is that the "metadata.calibre" file was being created when books were added to the reader, filled with the transferred book information. It was still there when calibre was shut down. Then when you fired up calibre again it would replace the contents of "metadata.calibre" with "[]" and show nothing for the device view.
The solution was to use the Preferences > Advanced > Plugins > Device Interface plugins > User Defined USB driver
(after first disabling the SONY PRST1 driver and using the "Customize plugin" procedure for the User Defined USB driver.) This also now recognizes the memory card and I'm now good to go.
Now we need to get collections to work.
I also noticed that you do not have to worry about thumbnails when creating a driver. What happens is that the Books.db is populated, along with a thumbnail being created by the Sony reader itself. This happens on the fly when viewing a book list by thumbnail on the reader for the first time. If you do not view the whole list, only the ones you view get generated and are available from then on whenever you view a book list.
I'll try to find out how collections are created next and let you know if I discover anything useful.
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