you'll see an 'Outline' tab. Click to that view and you'll have a far better way of viewing the site. You cab collapse the directories right back to the 'Home' folder if you want to.
Breaking the odd link is the least of your worries I should think - this sounds like an absolutely huge site - 18 hours to import is astounding, and in all the years I've worked on web design I have never know even the largest site take anything remotely as long as that. What size is the site on disk as a matter of interest? When you upload to the server I should start it off and go to bed, or take a weekend break.
I'm sure you have the site backed up to a CD, but if you don't I suggest doing so immediately, before you do any more work in NOF.
By all means come back to this thread with future questions - don't start any more new threads.