I can't add/remove apps through iTunes.

I wanted to sync my apps with iTunes, as I haven't got the iTunes app on my iPhone (don't know how I did that either lol) and I also wanted it for some other stuff. Now the box 'Sync Apps' is unchecked, and when I check it iTunes warns me that every app and content of that app will be removed and replaced by the apps in the iTunes library.. I'm really not that keen on losing data in Whatsapp for instance, as my memory depends on that app, lol.
Anyway, is there any possibility that I can add/remove apps through iTunes without losing data on my iphone? Maybe by making some sort of backup?
I really hope there's someone with an answer to this one, as I'm really out of ideas to solve this.
Thanks,
Axel

Guess what I didn't lose any data, not even in for instance games like Coin Dozer or Whatsapp or anything! I don't know how, but it's true! I didn't even have to re-login Wordfeud! Hurray!

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