I might be missing something, but I think this should help.
If you add a book to calibre, it adds it to the database and puts it into the library directory structure. If you then change the author or title in calibre, calibre will update the database and rename/move the book to reflect the changes. But, it doesn't update the metadata in the book. This can be done via a conversion or using the Modify ePub plugin (I prefer the latter). Calibre will also update the book when you do a save to disk or send to a device, but it only updates the new copy created, not the one in the library.
If you get a new copy of a book, or have done the save to disk that you mention, you can replace the copy in the calibre library. Find the book in calibre and select it. Then drag and drop the new copy onto the details pane for the book. If the book is of the same format as one already there, it will replace that. You can also do this via the edit metadata dialog.
As you are accessing your library via FTP, maybe you should consider running calibre in server mode. You can then browse and download books. I'm not an expert in this, but there is discussion about this here and in the user manual.
If we've missed something, maybe you can rephrase the question.