To do what you want I use the Kobo desktop app. Like the devices, this automatically downloads all new books. Then I delete them from the library. This then removes the book from the "I'm Reading" list on the site. Anything not on that list, will not be downloaded to the device. And will be removed at the next sync if it already is on it. If the device is connected when doing this, it will be removed from the device immediately.
The other thing you can do, and I'm surprised taming didn't mention it, is to let calibre manage the shelves. To do this, let the device sync the new book. And add the epub version to calibre. At the next sync with calibre, the books should get matched and the shelves set up.
The only problem with this is that the title and author of the two versions of the books have to match exactly. If there is a mismatch in some way, it doesn't work. But, you can fix it in calibre for the next sync.