You will if they aren't in your iTunes library. iTunes will erase all iTunes media from the phone and replace it with the media in the library you are syncing with. If you don't have or care about your app data, just download the new apps to your library before syncing (see http://support.apple.com/kb/HT2519). The apps will first be deleted, but then synced back to your phone when you sync. If you want to keep your app data, follow this guide: https://discussions.apple.com/docs/DOC-3141.