After thought, I changed calibre so that if you send a book to a device that is already on the device (UUID and extension match), the file name for the book already on the device is used and that file on the device is overwritten with the new content. The template and the UUID option are ignored. This change will go far to prevent duplicate book files when metadata changes.
If you don't like this change then you can shut it off by going to the smart device plugin and unchecking the option. I would be interested in hearing why you don't like the new behavior. I haven't been able to come up with a good reason to want more than one copy of a specific format of a book on the device, and there are lots of reasons to avoid it. The only reason I came up with is someone requiring that a file name on the device reflect the newest metadata, but this can be achieved by deleting the old file before sending the new one.
The UUID option remains necessary for people who have multiple devices and want the same file name on all regardless of how the book got to a particular device.
The replace-file behavior and the option will be in calibre 0.9.15. The next version of CC will support the UUID option. The UUID option will be ignored unless calibre is at release 0.9.15 or later.