This sounds to me like a pure database/technical problem. For some reason the book was flagged as available and during the transactions, it becomes not available some way, or ... the book's status changed while you were ordering. Book status can change because the store decided to take it out or any other legal problems. Even though I prefer the Kindle 3 and actually own one, I think this problem is a minor one on today's online bookstore databases.
But you are lucky! You paid with your AMEX. I've never feel abandoned with my AMEX. They will fight for you: get your money back or act as a middle man with B&N. I would also give a call to B&N and check status.
Bottom line: always back up your Kindle, Nook or whatever content you have!
And when I mean, backup is outside the device. Moreover, remove the DRM protection (if not illegal in your country) so you can actually own the book.