apps won't sync

[Cov]

I recently had to reinstall software on my macbook (i overran the hard drive). I bought an external to deal with the problem and now i am running fine. My iPhone is now not syncing the apps. My itunes store account is authorized, when I click the tab to sync the apps, it says that all the apps on my phone will be erased and replaced with the ones on this account. However, there are none listed in the apps window for itunes. If I sync, am I going to lose all my apps? Please help!!!