i'm not really sure what benefit you think they're gaining by breaking the less convenient, less user-friendly way to sideload books.
They're perfectly happy to let you email books to the kindle that you bought at other stores (or stole), as well as sync your progress with those books, backup those books to their servers, and generally have the full reading experience with all the benefits of the kindle ecosystem even if you didn't buy the book through kindle. If they didn't want to encourage the use of third-party files, surely they'd make it more difficult than a bug that randomly deletes books off some people's kindles sometimes.
The benefit (or potential gain) is that some people will just buy the book from the Kindle store to avoid the pain. I've seen that happen first-hand to my wife.
Also by emailing books or loading through their servers, they can still track and get that sweet sweet data/metadata that Amazon thrives on. When you sideload, you don't even have to connect it to the internet, which makes analytics more challenging.
They're perfectly happy to let you email books to the kindle that you bought at other stores (or stole), as well as sync your progress with those books, backup those books to their servers, and generally have the full reading experience with all the benefits of the kindle ecosystem even if you didn't buy the book through kindle. If they didn't want to encourage the use of third-party files, surely they'd make it more difficult than a bug that randomly deletes books off some people's kindles sometimes.