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Ughh... Looking at the output, your library is hooped.
The only time I saw a mess like that was when the library was stored in Dropbox. I'm wondering if your external hard drive is having issues considering the missing book files, duplicate book IDs, etc..
I'd suggest your best procedure is to close calibre, rename the library directory, open calibre, add a new library and import your old library to the new library using Add books => from folders and sub-folders. Not sure if the default assume books in the same folder are multiple formats of the same book should be on or off.
Perhaps running a search for your ebook file formats on the old library to see if the number of books that are imported to the new library comes close to matching the number in the old library.
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