It is a fact of life that if you run a busy regularly-updated website you'll also move your files about quite often. Whilst this may not pose a problem for you initially, search engines take a while to process dead links, and during this time you may be losing visitors who go to your old pages and get the standard 'page not found' error. You can prevent this by customizing your error pages, sending your visitors instead to a nice formatted webpage that politely tells them to keep on looking using your new navigation structure.