Amazon has made an announcement about the deregistration and factory reset issue on the Kindle Help Community forum:
If you’re having trouble finding your photos, apps, or other content on your Kindle Fire HD 8.9”, please check your current registration status by swiping down from the top of the screen, selecting More, and then selecting My Account. If your device is not registered, tap the Register button and then enter your Amazon account information. After you register your device, you may need to download your content again. To learn more, go to http://www.amazon.com/gp/help/customer/display.html?nodeId=201730090.
That link takes you to the Sync and Download Content to Your Kindle Fire page, There you will find instructions for syncing your content to your device:
To sync all content: With wireless connected, swipe down from the top of the screen to show Quick Settings, and then tap Sync.
The Sync Across Fire & Kindle Devices and Apps page implies that whether or not this restores bookmarks, highlights, etc., may depend on whether you have Whispersync enabled on your devices.
FYI: The Kindle Help Community forum is the one that is moderated by Amazon representatives. It is not the same as the Amazon customer forums where customers comment and attempt to help other customers.