You're trying to access the directory Calibre uses as a library directly. That's not how Calibre is intended to work. See
this post for details- it's far better written than anything I'd come up with.
EDIT: I'll try anyway, in short: Don't access the Calibre library in any other way than through Calibre itself- it's best viewed as a "black box" and left alone. Use the "Save to disk"- function to get your book to disk, then it'll do what you specified. Or transfer directly to your reader, both Sonys you have should be supported.