When I first installed Calibre, it prompted me for the folder to use for my ebooks. I didn't know it would make copies of every existing ebook. I assumed that I should tell it to use the folder I'm already using - the folder that already contained my ebooks. I assumed that like with MP3 database programs like Winamp, or Mediamonkey, or I tunes, or with photo database programs, the program creates mappings to the files.
That's where my disaster occurred. Calibre created an entirely new structure of folders in the existing structure of folders, with a duplicate for every book. The initial folder structure I had is totally hosed, as there is no way to extract the new folders that I can see. It's fine that it needs to create copies, but there should be a warning about this.
Imagine if you installed I-tunes and it duplicated all your music in the same folder structure as your existing music. You'd be surprised and pissed off.
I like the program, but I think this is an area that needs work - at least warn people that this can happen.