Gmail has done major overhauls all in one go. So has Dropbox. Google calendars. Google earth. Apple's main site. Most newspaper's sites. Bitbucket. Facebook has had several. All of these have irritated some portion of users who decried the death of the product, yet eventually people get used to it. I think it works more often than not.
And if we went suddenly from Amazon of five years ago[1] to the Amazon of today I don't think there would be that much of an uproar. It's basically the same site, just with minor colour and layout changes.
[1]: https://web.archive.org/web/20130316112319/http://www.amazon...