Problem with syncing

I had to re-install operating system, so everything in my iTunes library was lost, and I had to reinstall iTunes too. After re-installing, and authorizing my computer, I downloaded some new apps and tried to sync them to my iPhone. But whenever I click the "sync applications/music/etc" button at the top, it will say: "Are you sure you want to sync applications/music/etc? All existing applications/music/etc and their data on the iPhone "my iPhonename" will be replaced with applications/music/etc from this iTunes library". Why does it say that? It never used to say that before. Before reinstalling iTunes I use to delete stuff from my mobile applications folder all the time even though they were on my iPhone, and it would sync just fine, only ADDING the new apps, NOT wiping my entire iPhone blank and replacing it with the few new apps. Does anyone know how to fix this? I want to keep all the apps along with their data on my iPhone, and only ADD the new apps/music/videos/etc.
Thanks.