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Okay, that is actually a step in the right direction.
Make a backup of your library. Even as messed up as it currently is it's still a good idea to make a backup. Keep it separate from the original backup.
Next, when you run Check Library what are the error messages that you get? Is it all Extra Title errors or are there others?
Starting with just the Extra Title errors, pick one and using Explorer navigate to the corresponding file folders within the Calibre library filesytem. NOTE: It's best to do this with Calibre closed. What files are listed in the folder? Is it just an ebook file and an opf file? Are there multiple copies of the ebook file?
--If it's just one ebook file and an opf file move the entire book folder out of the Calibre library folder. Remember where you moved it to.
---Next, in Calibre use Add Book from single directory to add the book that you just moved out of Calibre. What happens? Was it added back in properly?
If there are multiple ebook and/or metadata.opf files things are going to be a bit more complicated and time consuming. Same if you are also getting Extra Book Formats or Unknown Files in Books error messages.
Go through the Extra Titles with a just a single ebook file first and see what happens. We can then tackle the others.
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