The second part I forgot for this is that maybe the metadata.calibre file was damaged. That should get used for the matching, but if it can't for some reason, then you see these sort of problems.
The manual match is done in the device list. Find an unmatched book, right click on it and select the match option. In the dialog search for the book, select it and press OK. Once you have fixed the matches, right click on the device button and choose the update metadata option. That will rewrite the metadata.calibre file.
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