Amazon is warning its iPhone, iPad and iPod touch Kindle app users to skip the version 3.6.1 update because it deletes purchases from the app. Users that already installed the update can re-download their missing ebooks, and the company said a new update is on the way.
Amazon's latest Kindle update clears ioS user's library
Amazon noted in its App Store Kindle description,
There is a known issue with this update. If you are an existing Kindle for iOS user, we recommend you do not install this update at this time.
If you haven't already updated to Kindle 3.6.1, avoid the Update All button in the App Store app so you don't accidentally find yourself with an empty ebook library. If you did install the update, you can re-login to your Amazon account in the Kindle app and add your ebooks back to your library.
Amazon hasn't said when the new update for the Kindle app will be available, and they are at Apple's mercy since it has to go through the review process before hitting the App Store.