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I bet that you used google drive at some point in this process. Google drive destroys calibre libraries by changing file names, removing the calibre ID that calibre puts into the book title. If your library is in google drive, get it out of it.
At this point the best way to fix things is to use calibre's library check. Click the arrow next to the library icon, go to Library Maintenance, and select Check Library. When it asks you if you want to check if the library matches the file system, choose Yes. You will see a dialog showing all the inconsistencies in the library. The books without the #### should show up as invalid titles. Check the boxes next to them and press Delete Marked.
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