According to Kobo CTO Trevor Hunter, a fix is in the works:
Kobo’s mandate of allowing people to read anytime, anywhere, on any platform remains unchanged. We are aware of the issue where a small percentage of books are not able to be backed up, and are working quickly to resolve it. We are currently working on other enhancements that will further embrace our open platform concept, which will give customers ever more options as it relates to reading and the backing up of ePub files.
Let's hope they come up with a permanent solution, because over the past few months there have been an increasing number of complaints about this problem. And to make matters worse, Kobo CS has described this issue not as a problem but as a feature. According to second hand reports from several sources, the reason people cannot download the ebooks is that they are Epub3 format. (This issue existed long before Epub3, so that is probably nonsense.)
There has been no pattern to the ebooks that are afflicted, with both DRMed ebooks and even DRM-free titles from Tor Books blocked from being downloaded at Kobo but still readily downloadable at other ebookstores.
There have in fact been so many complaints that yesterday I was inspired to post a solution in the form of a calibre plugin which stripped the DRM from your Kobo purchases, converted them to standard Epub, and loaded them into your calibre library.
Isn't it a shame that DRM made it necessary to jump throw hoops just so we could read the ebooks in the app we prefer?
image by clarle