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Try creating a new empty library and importing all your books, using:
Add books ==> Add books from directories, including subdirectories (one book per directory, assumes every ebook file is the same book in a different format)
This will fix any problems with moved records that the multiple versions of the database can't keep track of. It should also only import one epub per record, and list all multiples with an option to either add or ignore. All metadata changes will be read from the metadata.opf not the files.
I use this if I didn't save to disk on linux but want to import into Windows anyway -- a library is basically a save-to-disk backup except that its a REALLY bad idea to touch with your ten-foot-pole -- it's very handy.
Granted, you will have to re-import all your books, but it can do that without your input while you do something else.
Also, if you have custom columns, use "copy structure from existing library" when creating the new library, so the import will save all your custom metadata.
Then, if you like the results, you can delete the old library.
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