By default, the Book Copy module will create a new book with the same exact name as the book it is copying. This can become confusing and actually caused one of the site developers to accidentally delete the original book, which was reference in menus and such and left the site in a weird state.
Had the name of the copy been something other than the name of the original, then this problem would never have occurred. I dug through the code but just couldn't seem to figure it out. Any help will be greatly appreciated. Thanks!