DO NOT Mess with the old Library
Start a NEW Library. Library(icon):Create Library: Empty...(Optional if you have custom columns you want to keep:Copy Structure)
Now:
Add books from directories,<The 1 book PER one>: (the old Library Top folder (the one with Author name folders)
This will take TIME and
disk space (you will need free space at or more than the existing). As an alternate: Move the existing Library to Portable Media to free up space. Flash drives are slow, so I don't recommend creating the New Library TO a Flash drive.