You're not going to lose all your data. What itunes is referring to are any libraries that are on your iphone. When its asking if you want to sync, it is talking about any music, videos, podcasts, ringtones etc. that may be on your device. Its telling you that syncing will wipe out this media and put the new "checked" media onto your phone.
What I do is set "manually manage music" clicked, and "only sync checked items"
That way, you can go into movies or apps and check which ones you want on there. The apps will sync complete with any user info and settings that you previously inputted on the phone, but you will indeed lose your music and other things - only on the first sync though. Once you have changed to manually manage music you won't lose your data anymore upon each sync.
Every signature I've ever had has been modified within days. This is all that's left.