Wouldn't it be best to test both the old and new navigation on new users instead? This would be the ideal testing condition for the website. You can also use the data from existing users for the old and new navigation to look at the impact of the change (especially if you have lots of existing users), but if you want a fair comparison, then try to eliminate as many of the variables as possible so that you are only comparing the navigation. However, I don't think it is very easy to isolate the impact of the navigation, because it will impact on other aspects of the website as well. You should really base your testing on the reasons for the redesign.