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I confess to confusion, because I think that what you are asking for already happens in many cases.
Calibre stores information about the books on a device in a file that is stored on the device. When you connect, it retrieves this information and compares it with the book files actually existing on the device. Books no longer there are removed. Books that are added are scanned to get their metadata.
The next thing that calibre does is attempt to match the books actually on the device with those in the library. A book matches if it has the same title/author (found in the book's metadata if calibre options permit that) or if it has the same unique ID (EPUB supports this, but I don't know if other formats do). Thus, a moved book will (or should) still be matched with the book in calibre. It is even possible that the same book could be stored multiple times on the device, and calibre will find these.
Clearly calibre can't arbitrarily decide that some random book on the device matches a book in the library. There must be some information in the book that calibre can use, and I think that calibre currently uses that information.
How does what calibre does today differ from what you are suggesting?
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