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@monkeyshoulder - try this if its not too late, after taking library backups
Create a New Library based on the existing library, then use the Copy to library->New Library (delete after copy) option from the existing library, the books 'left behind' should be the ones that are 'missing'. The "Copy to library' action is probably in the book list context menu.
Switch to New Library and Remove the 'left behind' library from calibre. Delete the files metadata.db and .json files in the 'left behind' folder (not strictly needed, but... tidier). Now use the "add books - one book per folder" option with the 'left behind' folder.
BR
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