How to manage Apps without wiping out your iPhone App data?
It sounds as though your iPhone and/or iTunes aren’t synced to each other. Unfortunately, for you to manage the apps on the iPhone from iTunes, the iPhone needs to be synced to iTunes. So you’ll have to go through this procedure at least once, and replace what’s on the iPhone w/ what’s in iTunes.

No way around that, but thankfully, any apps you’ve purchased are free to you to download again, so if there are any that are missing in iTunes, just download them again.

But yes, if any of the apps aren’t in iTunes, and you’ve got data stored in those apps, that data will be lost.