I recently upgraded one of my site from Drupal 5 to Drupal 6 and found that the books and book pages were lost. I saw in Admin >> Content section that the content was there only the structure was lost.

Upon manually trying to recreate the books I was getting Duplicate error, so even the manual option was not working. It seems that this was a common error for many people

I did some reading and found many people have done some complex things to get around it. Let me tell you what worked for me.

Step I . I did the following steps mentioned on http://drupal.org/node/645214a#comment-2454738

1.) drop table book in D6 (if there are no diffs to your backup of D5)
2.) reimport table book from D5
3.) run update_6000 for the book module (2nd page of update, Select Version, choose 6000 in the drop-down-box for book)
4.) check your book hirarchy

Step II : I was geting some duplicates in book navigation , so I deleted the duplicated entry for top level page from menu_links table. The entries to be deleted are the ones which has “has_children” = 0 and not 1. Remember this was only for my Top level book page.

And everything else worked like charm.

This is a bug from the core team and I sincerely hope its fixed in D7 upgrade