How to backup iPhone to iTunes for the first time (data stored on the iPhone, not on iTunes)
Yes, if you do a direct sync, your apps will be wiped out. You should transfer the apps to the new iTunes by doing this:


  Files -> Transfer Purchases from iPod


This step should transfer your apps to iTunes. You can also see this Apple.SE post for a similar situation. After transfering purchases, you should then be able to sync with the new iTunes without losing your apps. The same situation holds for music.