Choose the "Replace device with list, add new items only" option. The add new items only means that if you have already sent an epub previously to the Kindle, it won't continually overwrite it. It should still remove from your Kindle any books that are no longer on the list, and of course add any items on the list not on the Kindle.
Make sure you don't have the "Clear this list after a sync to this device" option checked, or else your list won't be any good to do this a second time
