You can do this by following these steps:
- In your book's Book Tools menu, select
Manage Published Uploads.
- Drag your PDF file onto the box under "Upload your books" that says "Drag your file here (or click to browse)". Alternatively, you can click on the box to select the file from a folder on your computer.
As soon as you upload the new document, it will be available to all your current readers, and that will be the document someone gets when they buy the book. There is no additional step to publish the new version.
Can't find your Book Tools menu? Here are some instructions: http://help.leanpub.com/author-help/how-do-i-find-my-book-tools-menu.