I've never used Click Funnels, but heard a lot about it, so not sure how flexible it is in terms of setting up the site structure and URL's. The big thing is where his backlinks are linking to. Are the majority of his backlinks going to his homepage or inner pages? If its the inner pages then you either need to build the new Click Funnels pages to be on the same URL's or if you can't do that make sure you 301 redirect the old ones to the new pages. Bare in mind, if you change his/her content on page drastically too across his whole site he might lose (or gain) rankings.