How do you rebuild books and area's?

Xenforo by default has this functionality as do all addon, but I cant find it for VW. Is this available?

What do you need to rebuild about them? Hierarchy? Page counts? Last update?

There is no such tool in VaultWiki. If any of the above breaks outside debug mode, the cause is treated as a bug and we rebuild the appropriate information during the upgrade process. I am not aware of a legitimate way to break the information that would warrant a tool; only bugs.

If you are experiencing a bug, please report the bug.

I wanted to rebuild books to get rid of the deleted pages that still displayed in the book.

The fastest way to do this might be to add ?nocache=1 to the URL, which runs the page with no caches. In some cases, this might also overwrite the existing cache.