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.
Related: Did your Fire tablet just de-register … again? June 17, 2016
Yesterday, Amazon announced an update for the Kindle Keyboard. This updates document and Whispersync features as well as Amazon Local offers for those who have Kindles with Special Offers.
From the Amazon forums:
We’re excited to let you know that we’ve started delivering a new, free software update for Kindle Keyboard over Wi-Fi, which will bring software enhancements and new features, including:
–Download your archived Personal Documents on Kindle Keyboard: You can now view and download your archived personal documents to your Kindle Keyboard conveniently anywhere at any time. Your personal documents will be stored in your Kindle library until you delete them from the Manage Your Kindle page at http://www.amazon.com/manageyourkindle.
–Whispersync for Personal Documents on Kindle Keyboard: Just as with Kindle books, Whispersync automatically synchronizes your last page read, bookmarks and annotations for personal documents (with the exception of PDFs) across the Kindle devices. Learn more about Kindle Personal Document Service on http://www.amazon.com/kindlepersonaldocuments.
–AmazonLocal deals – Kindle Keyboard with Special Offers users in many regions can now view, purchase and redeem AmazonLocal deals directly from Kindle Keyboard – no computer, no printer, no hassle. AmazonLocal offers savings up to 75% off products and services from businesses in your city, national chains and online merchants. Learn more about AmazonLocal on http://www.amazonlocal.com.
To receive the update, turn your wireless on and connect to an available Wi-Fi network. From the Home screen, press Menu and select “Sync and Check for Items.” The software update will automatically download in the background and install the next time your Kindle goes into sleep mode. You can also manually download the update to your Kindle. You can learn more and download the update at http://www.amazon.com/kindlesoftwareupdates.