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Once you had found the "unmatched" books did you try right-clicking the book in Device View and using "Match book to Library" ? That should have allowed you to locate the Library book that matched the one on the device and then "connect" the two. Don't forget to update Metadata on device after matching. I found that after doing this the "Waiting Metadata Update" flag still shows - I then used Kobo Utilities to "Refesh List of Books on Device" to clear the flag and show the book as matched.
An easy way to find all the unmatched books is to sort on the "In Library" column while in Device View, then go to the end where all the unmatched books should be together.
Just some ideas to speed up the clean-up !
BobC
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