I wonder if the change has anything to do with the Paypal issue and SW are mass-purging removed books as a result. I would still encourage mass complaining as apparently SW had a ridiculous T&C clause derided in another thread which was officially interpreted by a CS staffer as forbidding Dropbox backup b/c SW would keep your books safe for you and you were supposed to re-d/l via their website alone.
As for Amazon, sometime last year or so I did read on their discussion board a complaint from a regular poster about how she'd lost archive access to several pulled original indie books and was out that money, IIRC. It shouldn't be too hard to find; I think I bookmarked it somewhere and she was a pretty prolific poster so should be easily Googleable for her handle and keywords if not.
Anyway, I would not place faith in any company whatsoever to keep books around, though Baen and FW have been pretty good about maintaining access to pulled MultiFormat stuff.