Some books I had on my wishlist disappeared when the new website came in. I emailed Kobo help about it and they acknowledged the problem, there are books that you can buy from the old website but not from the new one. Hopefully it will be fixed soon.
Example is
Raising the Stones by Sheri S. Tepper. The new website shows me a message saying that this book is no longer available.
The interesting thing is that I can still see this book in the bookstore on my Glo, and I assume I could buy it from my Glo. I am just a bit wary because if I can't see it on the website then will I be able to download the plain epub version?
I have also noticed that some books have different covers shown in the device's bookstore than on the new website, perhaps it is showing a different version of the book to the one I would get if I bought from the new website.