Actually, this is a good question. Did you ask the question, or search for a thread on the k3b forum? The last I read, an xcopy like feature is not available yet, but I would assume that you need to use the proper media size dvd-r to the one that you are backing up (assuming that your drive supports the larger size media). Otherwise, copy the dvd to a directory (if it is just a data dvd) on the hard drive and burn 2 single copies that match your media size on the dvd.
Also, if there are any hidden files on the dvd, then make sure you enable this option in k3b, to include these files.