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Actually, come to think of it, the file-matching process can have even simpler logic:
Assume that Calibre keeps a note that a given file was on a given device last time it was connected to that device. Now, that device is connected and that file is still in calibre's library but isn't seen on the device (due to a different title/author/file path or name or whatever calibre keys on). That device also contains one or more files which are not in calibre's library.
Match the first group of files (in library, not on device) against the second ground (on device, not in library) using actual file data (CRC, say). If a match is found, link the library entry to the device entry.
That should do it.
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