According to reports, the update is causing users' entire book libraries to be deleted from their devices. There is no word yet on when a fix can be expected to arrive in the App Store, but Amazon is undoubtedly rushing to fix the issue and Apple is likely to provide an expedited review in order to minimize the number of affected users.What's New in Version 3.6.1
Note: 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.
Update 7:29 AM: AllThingsD reports that Amazon has issued a statement indicating that it has submitted a fix for the issue to Apple and is working to expedite its release.
Update 9:36 AM: Kindle for iOS has been updated to version 3.6.2, presumably addressing the issue with version 3.6.1. The new release notes do not, however, mention the issue.
Article Link: Amazon Warns Against Installing Latest Kindle App Update for iOS Due to Deleted Book Libraries [Update: Fix Live]