calibre should automatically rename files in its library, when you change metadata.
(But if it isn't
then I suppose you could always save-to-disk and then re-import using Add books ==> Multiple books per directory, assumes every file is the same book in a different format. That uses the metadata.opf to derive the full set of calibre metadata.)
Sorry about the ghost books
I don't usually get them unless I am not careful... but then again, I've played around enough to know how not to mess up. Also my information may be dated just like my ereader.
For instance, I have no idea how Cloud Collections may impact things...