They have deleted books, but I only remember for good reasons. The famous 1984 deletion was because the publisher didn't actually have copyright, which seems like as good as of a reason as a company can have.
They also said they'd never do something like that again. Bezos personally apologized for the way Kindle users were affected by the 1984 incident.
AFAIK, Apple has never owned up to one of its policy decisions having been a mistake, let alone apologized for it. They've changed their policies -- witness the short-lived language choice terms -- but never issued anything even suggestive of a mea culpa.
In my opinion, there cannot be a good reason for pulling books that you bought, ever.
Imagine that happening to dead-tree books, someone shows up on your doorstep to reclaim the book 'because it violates copyright'. You'd tell them to bugger off, and it's no different in this case.
Once you bought a book, digital or analog, it should stay in your possession for as long as you want.
