This happend to my kindle to! After keeping in in flight mode for years I put it online again in order to buy a few new books from the kindle store, poof suddenly my entire library of side loaded books was gone, with progress and everything. I could see random metadata files related to the books on the drive, be books was gone. Super annoying as many of the books I didn't have locally anymore and to loose the "archivement" of finished books sucks big time.
I can see this may be implemented by amazon to counter piracy, but alot of these books was perfectly legal.
So the result of this is that I will never put my kindle online again and just stop buying from the Kindle store.
Keep mine in Aeroplane mode. Download books I buy on Amazon directly from amazon and drop them into calibre. Amazon doesn't get to touch my Kindle ever.
Thinking hard if I ever want to get another Kindle when Amazon can just screw around with what I put on my Kindle ...
Same, though I don't think it is going to help Amazon the way they hope it does. I moved books over to my kindle and had it nuke my humble bundle collections when I added a purchase from Amazon. I've not connect it again until I figure out how to backup and restore MY metadata.