Right so I had a major problem and my library was gone. I used Library Management to rebuild the database and voila they re-appeared. With an exception and two, and fine. But help, help, help. My Collection and my Shelves are gone! I have over 21,000 books, a lot of them fanfic

and just the thought of having to re-label them all makes me faint. I also had to create my own columns for Shelves and Collections and formats. None of which appeared when I upgraded Calibre.
Instead there are idiotic ratings, publisher etc that I really don't need. I've updated to the latest 3.42 Calibre.