This one's coming straight from the horse's mouth. Amazon is acknowledging a "known issue" with version 3.6.1 of its Kindle app for iOS -- the company is recommending that current users avoid the latest update, which hit the App Store today. According to TUAW, the new version may completely erase a user's book library. How this passed the e-book giant's QA team is anyone's guess, but until a revision hits the cloud, we suggest you stay away.
Update: Amazon has reached out to clarify this issue. The update causes the app to "deregister," and as a result, items are removed from the smartphone or tablet. All of your content remains in the cloud, however, and can be re-downloaded after you re-register the device with Amazon. The update has been re-submitted to Apple and should appear soon. Consider us re-lieved. You'll find the official word below:
We have identified an issue with the app update that may cause your app to become deregistered. To register, enter your Amazon account e-mail address and password and all your Amazon content will be available in the cloud. We have submitted an update fix for this issue and are working with Apple to release.
Update 2: As of Wednesday afternoon, the app has been replaced with version 3.6.2, with listed improvements including "Fix for Registration Issue." The source link will now direct you to that latest version, which, presumably, won't make all your books disappear.
Source: Amazon (iTunes)