It is interesting that restoring the sqlite database doesn't include the 100 free books. I thought that the "virgin" sqlite database only restored the 100 free books. You may want to check if you have the settings to not show them (go to your books menu, not I'm reading menu, then push the display button, 3rd button from top, and you should have a screen that now gives you the option under books to display "all books" or "my books". If you choose "all books" the 100 free books and added books will show, if you have only my books the 100 books will be hidden).
Sorry if you'r already aware of this and it isn't the problem.