How does the Download Tool Work?
Let's have a quick look at what the eBook Downloader actually does. We have nothing to hide about it, and want to demonstrate that it doesn't in fact remove any DRM.
So let's look at the HTML source of the Kindle Cloud Reader. If you go to read.amazon.com, select one of your books, and press the F12 key, a new browser window opens, in which you can navigate the HTML source of the Cloud Reader. If you navigate through the source, you'll eventually find the content of the page that's currently being displayed.
Here you can right click on a specific element, or the <html> root that contains this content, and copy that node as HTML. If you paste it to a new text document, you've successfully managed to accomplish what the download tool can achieve with a single click.
As you can see, this tool merely provides a semi-automated way of executing a small number of manual steps. We do not break any DRM, but simply copy and paste the unencrypted HTML source of the Kindle book.