They'll be hidden inside your file now. If you reset it and then restore, they'll come back.
On a Windows machine, if you go Start > Accessories, you should have Address book. My contacts are all in there. Can't remember how/why/when, but they are.
So you could do a fresh install and then just put that stuff back. Then re-add the apps etc manually.
Otherwise your only option is to re-jailbreak and fix all your settings back to normal before you restore.