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Thank you Jack and David.
Fortunately I have some backups with Calibre and Kobo Utilities. It looks like my only solution will be to identify the books that I added within Calibre, then to remove them en masse. Finally add the books back a few at a time.
The Date field in Calibre seems to be the date added, and I have identified the 66 books added on the same day recently. I will remove them and see how I go.
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