Due to a new policy, ChristianBook.com will no longer allow you to download your ebooks from them, if you added them during a free promotional period (ie, if they were "free" when you "purchased" them). I just ran into the new policy by chance, when I tried to download what was marked as a DRM-Free EPUB that I purchased today -- and found my entire library was no read online only. They claim this change is due to the added costs of serving out free books, but their decision applies equally to books that are DRM-free, where the only cost is bandwidth and that cost won't change by using their app. From now on, you will be required to read any freebies obtained from them using one of their proprietary apps (and I don't know about you, but I have gotten to where I refuse to install another app just to read a free book, especially one that I can get elsewhere and very much especially if I have to be online to do the reading). I hope everyone had a backup of their libraries there, as this is a retroactive decision, applying to all the books you have purchased (I just downloaded a couple of them last weekend, which I didn't have as an EPUB elsewhere, but I'm sure I will have lost at least a couple of books due to their decision).
They aren't the only ones making unannounced and unilateral changes to their libraries. Jasmine Jade used to be the store site for Ellora's Cave and when they moved everything back to their Ellora's Cave site, some libraries made it over and others did not (mine was one of the ones that did not). They are super nice and will help with redownloading any book you didn't back up, but you'll need to email them on each one (and probably provide your old order number). When Borders Bookstore closed, they transferred my library to Kobo - it was painless and took a couple of clicks; but when Fictionwise announced that they were closing, the process was apparently designed to work as badly as possible. You were supposed to sign up after receiving an email, then wait (some unspecified length of time) before you then responded again to a new email with a magical code in it. Then, all but a few books, listed titles would appear in your B&N account. The only problem - apparently they are doing everything by hand and many, including myself, are still waiting for a code to continue the process. Others managed to get thru that step, but still waited weeks for any of their books to appear. And that limited list of titles - it keeps growing every time I check it (and now they have a PDF linked that promises to list even more excluded titles). Contrast this to the process when Peanut Press and subsequent sites were purchased and rolled up to ereader.com -- my account and books moved along without me for several years, until I rediscovered the account, complete with every book I had purchased along the way (on my old palm devices/phone).
It's not only due to decisions of the site that you can lose access. In the last couple of weeks, DelphiClassics claims to have had their files deleted by their web hosting company. Since they apparently had their backups at the same location, they lost those as well (OK, who doesn't know that it's a bad idea to store all of your backups in the same location as your main copy?). If you didn't make a backup, you may be out of luck, unless an update to one of your purchases happens in the next year. In that case and if you kept track of your receipt, so you have the order number, you can follow these directions to request an update for that one particular title. Yes, your old purchase supposedly came with lifetime updates (and new ones don't), but that's as far as they are willing to go for past purchases.
Let these be a cautionary tale, if not a lesson, in why you should be downloading all of your ebooks up on purchase and keeping a copy (or two) somewhere safe. You should consider saving your emailed receipts, also (at the very least, keep them in a folder in your email client, but consider saving them to your hard drive, together in a folder, as well), in case you need to refer back to them in order to get your library restored. I've even had one or two (as far as I know, only about that many) books at Amazon that have completely switched content after the initial purchase and download (title changed and all) and had to use an old receipt to get them to investigate and fix my library (usually by having to repurchase the book, after they applied a promo code).