My Harddrive Failed and Now I can't Sync with iTunes

My hard drive crashed and was just replaced by apple. I have a jailbroken 4s, and I am trying to sync with my new itunes on my new hard drive. I perform all the steps to sync with my iphone(authorize, backup...etc). It syncs my contacts, calendar, and some of my apps. Some of my jailbroken apps went over, but most are not. How can I sync all of them? Now when I check the "Sync Apps" check box it says that all my iphone apps will be replaced by the apps on my itunes. How do I get them to merge?

Any help would greatly be appreciated.

Thanks

That was one of the steps I took when I tried to sync the first time...just tried it again anyway and same result. No new apps transfered over.