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@wladdy - sorry I can't offer any insight on the error message, other than the obvious. I've only used the command to 'hurry things along' when I've changed something like Publisher that cascaded through '000s of books.
One suggestion (if not already tried) - try using the Copy to Library feature (you may need to add it to a Toolbar) to Move (Copy with delete) all the books in the Book list to a fresh library. That should leave the library with a set of "left over" author/book folders that need "sorting out".
First I would remove the old library from calibre (Library->Remove Library), it wont delete anything there, just lose sight of it. Then I would manually deal with the "left over" books - how I did that would depend on how many there were, what files existed and the mood I was in.
BR
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